CD47

Summary

CD47 (CD47 molecule, HGNC:1682) is a protein-coding gene on chromosome 3q13.12, encoding Leukocyte surface antigen CD47 (Q08722). Adhesive protein that mediates cell-to-cell interactions.

This gene encodes a membrane protein, which is involved in the increase in intracellular calcium concentration that occurs upon cell adhesion to extracellular matrix. The encoded protein is also a receptor for the C-terminal cell binding domain of thrombospondin, and it may play a role in membrane transport and signal transduction. This gene has broad tissue distribution, and is reduced in expression on Rh erythrocytes. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 961 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 63 total
• GTEx eGene: eQTL in 29 tissues, sQTL in 10 (q < 0.05)
• Drug target: yes — 2 curated mechanism-of-action drugs
• Constraint (gnomAD): pLI 0.76 (intermediate), LOEUF 0.72 (unconstrained)
• MANE Select transcript: NM_001777
• Interaction hub: 2,708 STRING partners (top 3% of genes corpus-wide)
• Notable: 63 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1682
Approved symbol	CD47
Name	CD47 molecule
Location	3q13.12
Locus type	gene with protein product
Status	Approved
Aliases	IAP, OA3
Ensembl gene	ENSG00000196776
Ensembl biotype	protein_coding
OMIM	601028
Entrez	961

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 29 protein_coding, 4 nonsense_mediated_decay, 1 retained_intron

MANE Select: ENST00000361309

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 2: 1, TSL 3: 1

ENST00000361309, ENST00000355354, ENST00000398258, ENST00000471694, ENST00000517766, ENST00000644850, ENST00000887585, ENST00000887586, ENST00000887587, ENST00000887588, ENST00000887589, ENST00000887590, ENST00000887591, ENST00000887592, ENST00000887593, ENST00000920144, ENST00000960414, ENST00000960415, ENST00000996835, ENST00000996836, ENST00000996837, ENST00000996838, ENST00000996839, ENST00001025723, ENST00001025724, ENST00001025725, ENST00001025726, ENST00001025727, ENST00001025728, ENST00001109443, ENST00001109444, ENST00001109445, ENST00001119566, ENST00001144942

RefSeq mRNA: 3 — MANE Select: NM_001777 NM_001382306, NM_001777, NM_198793

CCDS: CCDS43125, CCDS43126

Canonical transcript exons

ENST00000361309 — 11 exons

Exon	Start	End
ENSE00000774901	108051939	108051970
ENSE00000774903	108058337	108058429
ENSE00000774904	108059452	108059544
ENSE00000774905	108060745	108060852
ENSE00000774906	108071093	108071182
ENSE00000823360	108079991	108080344
ENSE00001369930	108049619	108049651
ENSE00001372086	108050578	108050602
ENSE00001840474	108043091	108047292
ENSE00001932120	108090863	108091031
ENSE00003526807	108057477	108057569

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 59.9116 / max 416.2548, expressed in 1816 samples.

Highest expression (Bgee): gingival epithelium, esophagus squamous epithelium, gingiva, palpebral conjunctiva, squamous epithelium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CD47 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 29 tissues and its splicing (sQTL) in 10 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 39 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells EBV-transformed lymphocytes	eqtl	5.0e-28	-1.12	3:108124634:C:T
Esophagus Mucosa	sqtl	3.6e-19	-0.49	3:108041953:A:G
Artery Tibial	eqtl	2.0e-16	-0.32	3:108071544:A:G
Thyroid	sqtl	6.7e-12	-0.32	3:108041953:A:G
Whole Blood	eqtl	4.3e-10	+0.10	3:108100194:G:A
Artery Aorta	eqtl	1.0e-09	-0.24	3:107895076:T:C
Cells Cultured fibroblasts	eqtl	1.6e-09	-0.17	3:107959740:C:T
Adipose Subcutaneous	eqtl	1.7e-08	-0.16	3:108084656:A:C
Colon Transverse	eqtl	6.0e-08	-0.30	3:108084656:A:C
Esophagus Muscularis	eqtl	1.1e-07	-0.24	3:107957227:A:G
Esophagus Mucosa	eqtl	4.0e-07	+0.14	3:107988611:T:C
Lung	sqtl	2.2e-06	-0.25	3:108080618:A:T
Stomach	sqtl	5.4e-06	-0.22	3:108075605:T:C
Skin Not Sun Exposed Suprapubic	sqtl	7.3e-06	+0.27	3:108056320:C:T
Esophagus Gastroesophageal Junction	eqtl	1.1e-05	-0.22	3:108071544:A:G
Skin Sun Exposed Lower leg	sqtl	1.4e-05	-0.29	3:108041953:A:G
Adipose Visceral Omentum	eqtl	1.6e-05	-0.16	3:108044193:G:A
Spleen	eqtl	4.6e-04	-0.65	3:107977440:G:A
Stomach	eqtl	1.2e-03	-0.20	3:107957227:A:G
Nerve Tibial	eqtl	1.3e-03	-0.12	3:107935814:G:A

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
43654	50.1872	1812
43655	8.3170	1733
43653	0.7527	400
43649	0.5227	266
43652	0.1182	47
43648	0.0137	4

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
gingival epithelium	UBERON:0001949	99.37	gold quality
esophagus squamous epithelium	UBERON:0006920	99.19	gold quality
gingiva	UBERON:0001828	99.17	gold quality
palpebral conjunctiva	UBERON:0001812	99.13	gold quality
squamous epithelium	UBERON:0006914	99.10	gold quality
germinal epithelium of ovary	UBERON:0001304	99.07	gold quality
visceral pleura	UBERON:0002401	98.98	gold quality
right uterine tube	UBERON:0001302	98.88	gold quality
epithelial cell of pancreas	CL:0000083	98.85	gold quality
epithelium of nasopharynx	UBERON:0001951	98.76	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.76	gold quality
tibia	UBERON:0000979	98.70	gold quality
oviduct epithelium	UBERON:0004804	98.70	gold quality
pancreatic ductal cell	CL:0002079	98.67	gold quality
epithelium of esophagus	UBERON:0001976	98.67	gold quality
postcentral gyrus	UBERON:0002581	98.64	gold quality
parietal lobe	UBERON:0001872	98.59	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.47	gold quality
cervix squamous epithelium	UBERON:0006922	98.46	gold quality
tendon of biceps brachii	UBERON:0008188	98.45	gold quality
pleura	UBERON:0000977	98.44	gold quality
pons	UBERON:0000988	98.43	gold quality
tongue squamous epithelium	UBERON:0006919	98.42	gold quality
lymph node	UBERON:0000029	98.38	gold quality
amniotic fluid	UBERON:0000173	98.33	gold quality
islet of Langerhans	UBERON:0000006	98.31	gold quality
vermiform appendix	UBERON:0001154	98.31	gold quality
endometrium epithelium	UBERON:0004811	98.31	gold quality
corpus callosum	UBERON:0002336	98.23	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.21	gold quality
substantia nigra pars compacta	UBERON:0001965	98.20	gold quality
granulocyte	CL:0000094	98.14	gold quality
parietal pleura	UBERON:0002400	98.12	gold quality
lower lobe of lung	UBERON:0008949	98.08	gold quality
cervix epithelium	UBERON:0004801	98.07	gold quality
type B pancreatic cell	CL:0000169	98.06	gold quality
tonsil	UBERON:0002372	98.06	gold quality
superior frontal gyrus	UBERON:0002661	98.05	gold quality
fallopian tube	UBERON:0003889	98.05	gold quality
middle temporal gyrus	UBERON:0002771	98.03	gold quality
choroid plexus epithelium	UBERON:0003911	98.02	gold quality
synovial joint	UBERON:0002217	98.01	gold quality
caecum	UBERON:0001153	97.99	gold quality
mouth mucosa	UBERON:0003729	97.98	gold quality
minor salivary gland	UBERON:0001830	97.96	gold quality
subthalamic nucleus	UBERON:0001906	97.96	gold quality
superior vestibular nucleus	UBERON:0007227	97.93	gold quality
sperm	CL:0000019	97.90	gold quality
trigeminal ganglion	UBERON:0001675	97.89	gold quality
right lung	UBERON:0002167	97.89	gold quality
lateral globus pallidus	UBERON:0002476	97.89	gold quality
upper lobe of lung	UBERON:0008948	97.88	gold quality
rectum	UBERON:0001052	97.87	gold quality
bronchial epithelial cell	CL:0002328	97.85	gold quality
gall bladder	UBERON:0002110	97.85	gold quality
upper lobe of left lung	UBERON:0008952	97.84	gold quality
bone marrow cell	CL:0002092	97.82	gold quality
lung	UBERON:0002048	97.80	gold quality
esophagus mucosa	UBERON:0002469	97.80	gold quality
saliva-secreting gland	UBERON:0001044	97.79	gold quality
bone marrow	UBERON:0002371	97.76	gold quality
globus pallidus	UBERON:0001875	97.63	gold quality
male germ cell	CL:0000015	97.62	gold quality
medial globus pallidus	UBERON:0002477	97.61	gold quality
trabecular bone tissue	UBERON:0002483	97.59	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.58	gold quality
entorhinal cortex	UBERON:0002728	97.49	gold quality
vagina	UBERON:0000996	97.48	gold quality
inferior vagus X ganglion	UBERON:0005363	97.42	gold quality
medulla oblongata	UBERON:0001896	97.38	gold quality
mucosa of transverse colon	UBERON:0004991	97.37	gold quality
calcaneal tendon	UBERON:0003701	97.34	gold quality
tendon	UBERON:0000043	97.32	gold quality
skin of hip	UBERON:0001554	97.31	gold quality
occipital lobe	UBERON:0002021	97.28	gold quality
pylorus	UBERON:0001166	97.27	gold quality
dorsal plus ventral thalamus	UBERON:0001897	97.27	gold quality
prostate gland	UBERON:0002367	97.20	gold quality
nasal cavity mucosa	UBERON:0001826	97.19	gold quality
epithelium of bronchus	UBERON:0002031	97.18	gold quality
olfactory bulb	UBERON:0002264	97.18	gold quality
bronchus	UBERON:0002185	97.14	gold quality
spleen	UBERON:0002106	97.12	gold quality
endothelial cell	CL:0000115	97.11	gold quality
primary visual cortex	UBERON:0002436	97.04	gold quality
ventral tegmental area	UBERON:0002691	97.03	gold quality
oral cavity	UBERON:0000167	97.00	gold quality
leukocyte	CL:0000738	96.99	gold quality
placenta	UBERON:0001987	96.94	gold quality
dorsal root ganglion	UBERON:0000044	96.93	gold quality
cardiac muscle of right atrium	UBERON:0003379	96.91	gold quality
mononuclear cell	CL:0000842	96.85	gold quality
monocyte	CL:0000576	96.84	gold quality
thyroid gland	UBERON:0002046	96.84	gold quality
left lobe of thyroid gland	UBERON:0001120	96.78	gold quality
lower esophagus mucosa	UBERON:0035834	96.77	gold quality
seminal vesicle	UBERON:0000998	96.66	gold quality
body of stomach	UBERON:0001161	96.65	gold quality
descending thoracic aorta	UBERON:0002345	96.64	gold quality
caput epididymis	UBERON:0004358	96.60	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	17.30
E-MTAB-9388	yes	11.75
E-MTAB-6678	yes	9.22
E-GEOD-130148	yes	6.73
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 78 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Retina	tissue	264.3
Bone marrow	tissue	219.0	low
Tonsil	tissue	151.2	medium
Putamen	tissue	146.5
Lung	tissue	145.6	not detected
Cerebral cortex	tissue	143.7	high
Occipital cortex	tissue	143.7
Somatosensory cortex	tissue	137.3
Motor cortex	tissue	137.2
Retrosplenial and cingulate cortex	tissue	133.9
Retrosplenial cortex	tissue	133.0
Prefrontal cortex	tissue	132.1
Basal ganglia	tissue	131.5	not detected
Lymph node	tissue	128.6	low
Cerebellum	tissue	125.7	high
Olfactory bulb	tissue	121.2
Hippocampal formation	tissue	117.2
Entorhinal cortex	tissue	117.2
Insular cortex	tissue	117.1
Ventral forebrain	tissue	114.6
Prostate	tissue	114.5	high
Temporal cortex	tissue	110.0
Appendix	tissue	109.6	low
Urinary bladder	tissue	102.7	high
Thalamus	tissue	102.1
Midbrain	tissue	102.0
Nucleus accumbens	tissue	101.2
Septum	tissue	99.9
Salivary gland	tissue	98.9	medium
Pons	tissue	98.4
Stomach 1	tissue	98.1	low
Postcentral gyrus	tissue	94.9
Fallopian tube	tissue	94.4	high
Spleen	tissue	94.2	low
Rectum	tissue	93.1	medium
Superior colliculi	tissue	90.5
Locus coeruleus	tissue	89.4
Caudate putamen	tissue	88.4
Esophagus	tissue	88.2	low
Epididymis	tissue	87.0	medium
Corpus callosum	tissue	86.4
Thyroid gland	tissue	85.3	low
Breast	tissue	83.4	medium
Colon	tissue	83.3	low
Gallbladder	tissue	81.3	low
Amygdala	tissue	78.3
Hypothalamus	tissue	77.0
Placenta	tissue	75.1	medium
Small intestine	tissue	74.5	low
Thymus	tissue	73.6
Hippocampus	tissue	71.7	not detected
Substantia nigra	tissue	71.3
Duodenum	tissue	70.1	not detected
Spinal cord	tissue	70.1
Medulla oblongata	tissue	68.8
Liver	tissue	66.6	not detected
Periaqueductal gray	tissue	66.4
Choroid plexus	tissue	66.3
Frontal cortex	tissue	64.5
Vagina	tissue	63.6	medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Corpus callosum, splenium (white matter) (157.3), Corpus callosum, genu (white matter) (153.5), Lateral funiculus (white matter) (143.2), Parieto-temporal junction (white matter) (142.3), Dorsal funiculus (white matter) (141.9).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NRF1, SPI1

miRNA regulators (miRDB)

Targeting CD47 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 236 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-3065-5P	99.97	71.56	3281

Functional genomics

gnomAD constraint: pLI 0.759, LOEUF 0.725, missense Z 0.945 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000361309 splits into 5 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
3:108,047,291–108,059,503	131 / 135.3	0.97	no
3:108,059,504–108,080,047	65 / 119.9	0.54	no
3:108,080,048–108,080,146	47 / 36.2	1.30	no
3:108,080,147–108,080,279	25 / 52.7	0.47	no
3:108,080,280–108,090,908	38 / 42.7	0.89	no

Literature-anchored findings (GeneRIF, showing 40)

• The Drosophila miR-959-962 Cluster Members Repress Toll Signaling to Regulate Antibacterial Defense during Bacterial Infection. (PMID:33477373)
• The interaction of CD47 with SHPS-1 may contribute to the recruitment of B lymphocytes via endothelial cells under steady state conditions. (PMID:11907074)
• Interactions of thrombospondins with alpha4beta1 integrin and CD47 differentially modulate T cell behavior (PMID:11980922)
• regulates integrin function. Differential effects on alpha vbeta 3 and alpha 4beta1 integrin-mediated adhesion. (PMID:12218055)
• mechanism of antigen-induced caspase-independent cell death in normal and leukemic cells (PMID:12351399)
• An autocrine loop of the integrin alpha(V)beta(3)/CD47 receptor complex and thrombospondin-1 is identified as the molecular coupling device between mechanical loading and apoptosis. (PMID:12370491)
• distribution of CD47, most restrained by cytoskeleton linkages plus a smaller fraction able to diffuse in the membrane, and colocalization with Rh protein complexes (PMID:12393442)
• Evidence protein 4.2 interacts with the Rh membrane complex member CD47 obtained from red cells of patients with hereditary spherocytosis associated with complete protein 4.2 deficiency (PMID:12393467)
• CD47 expressed on platelets significantly contributes to platelet adhesion on tumor necrosis factor-alpha (TNF-alpha)-stimulated vascular endothelial cells (PMID:12609828)
• Ligation of CD47 by any of its known ligands rapidly induces heterotrimeric Gi alpha-dependent but caspase-independent apoptosis in Jurkat T cells and, importantly, in activated primary T cells. (PMID:12646616)
• the extracellular Ig domain of IAP(CD47), when bound to thrombospondin, interacts with integrin alphaIIbbeta3 and can change alphaIIbbeta3 in a high affinity state without the requirement of intracellular signaling (PMID:12736272)
• Interaction of CD47 with thrombospondin-1 contributes to the perpetuation of inflammation in rheumatoid synovitis. (PMID:12902472)
• protein 4.2 strongly influences CD47 levels as well as the extent of membrane skeleton attachment in erythrocytes (PMID:14551146)
• IAP gene expression is regulated by alpha-Pal (PMID:14747477)
• CD47 recruits alpha(v)beta(3) and its associated signaling molecules to these domains (PMID:14966135)
• CD47 has a role in inducing alpha4beta1 integrin activation and adhesion in sickle reticulocytes (PMID:15292185)
• Review. The interaction between CD47 and SIRPalpha seems to be important to limit destruction of host cells in autoimmune diseases like autoimmune hemolytic anemia (AIHA), where macrophages destroy antibody or complement opsonized cells. (PMID:15359629)
• CD47 short interferint RNA inhibited cell proliferation in cultures of hepatoma cells. (PMID:15498560)
• Apoptosis inducing single-chain antibody fragments against cd47 antigens will be effective as a novel therapy for multiple myeloma. (PMID:15725479)
• SHPS-1 negatively regulates platelet function via CD47, especially alpha(IIb)beta(3)-mediated outside-in signaling (PMID:15842360)
• Novel CD47-dependent intercellular adhesion modulates cell movement. (PMID:15880429)
• CD47 associates with Fas upon its activation and augments Fas-mediated apoptosis. (PMID:15917238)
• SIRPalpha-CD47 interactions, which reportedly define self, exhibit cell type specificity and limited cross-species reactivity (PMID:16291597)
• RhD co-localizeS with CD47 but not calreticulin or glycophorin-A on human RBCs. (PMID:16581280)
• highlight major species differences in CD47-SIRPalpha interactions and CD47 integration, suggesting that signaling by CD47 in man may be qualitatively different from mouse. (PMID:16697668)
• CD47 stimulation by a thrombospondin-1 peptide induces naive or memory CD4+CD25- T cells to become suppressive. (PMID:16951312)
• analysis of species-specific CD47 interactions with signal regulatory protein alpha (PMID:17098740)
• Genetic induction of human CD47 on porcine cells could provide inhibitory signaling to SIRPalpha on human macrophages, providing a novel approach to preventing macrophage-mediated xenograft rejection. (PMID:17360380)
• In this review the authors provide mechanistic insight into the signaling pathways used by thrombospondin-1 and CD47 at the cellular and molecular level to prevent nitric oxide signaling through cyclic GMP, thereby exacerbating tissue ischemia. (PMID:17363705)
• Upregulation of CD47 in sporadic inclusion body myositis. (PMID:17572512)
• CD47/IAP is necessary for chondrocyte mechanotransduction. Through interactions with alpha5beta1 integrin and thrombospondin, CD47/IAP may modulate chondrocyte responses to mechanical signals. (PMID:18186923)
• On both RBCs and microbeads, human CD47 potently inhibits phagocytosis as does direct inhibition of myosin. CD47-SIRPalpha interaction initiates a dephosphorylation cascade directed in part at phosphotyrosine in myosin. (PMID:18332220)
• CD47 may play an inhibitory role in NK cell-mediated cytotoxicity against cancer cells, implying a possible mechanism of immune escape in human cancer. (PMID:18497546)
• A T cell-negative sensor that may serve to dampen unchecked proinflammatory T helper cell type 1 (Th1) responses, such as occur during contact hypersensitivity in transgenic mice. (PMID:18523271)
• CD47 is enriched at endothelial junctions, and its interaction with SIRPgamma is required for human T-cell transendothelial migration (PMID:18524990)
• These results explain the specificity of CD47 for the SIRP family of paired receptors in atomic detail. (PMID:18657508)
• TSP-1’s C-terminal domain opens to interact with the CD-47 receptor (PMID:18675774)
• In this review, the CD47/thrombospondin-1/signal-regulatory protein (SIRP)-alpha inhibitory axis is proposed as an important sensor to maintain homeostasis and regulate innate and adaptive immune responses. (PMID:18855618)
• Expression levels of CD47, CD35, CD55, and CD59 on red blood cells and signal-regulatory protein-alpha,beta on monocytes from patients with warm autoimmune hemolytic anemia. (PMID:18954403)
• Down-regulation of the IAP antagonistis XAF1, Smac/DIABLO and HtrA2, has been related to the onset and progression of various malignancies. (PMID:18979398)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cd47	ENSMUSG00000055447
rattus_norvegicus	Cd47	ENSRNOG00000001964
rattus_norvegicus	LOC100909977	ENSRNOG00000042598

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:96617) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 50 distinct phenotype terms.

Mouse phenotype (MP)	Records
decreased hematocrit	2
increased susceptibility to bacterial infection	2
decreased leukocyte cell number	1
decreased neutrophil cell number	1
increased bone marrow cell number	1
abnormal hindlimb morphology	1
abnormal spleen morphology	1
enlarged spleen	1
decreased sensitivity to skin irradiation	1
abnormal skeleton physiology	1
hemolytic anemia	1
decreased tumor incidence	1
premature death	1
abnormal neutrophil physiology	1
impaired neutrophil phagocytosis	1
behavioral despair	1
increased heart rate	1
reticulocytosis	1
abnormal passive avoidance behavior	1
decreased hemoglobin content	1
abnormal excitatory postsynaptic potential	1
thrombocytopenia	1
abnormal physiological neovascularization	1
abnormal bone structure	1
abnormal muscle fiber morphology	1

+25 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pongo abelii	Q5REL0	99.4%	Diamond
Sus scrofa	Q9GKE8	82.8%	Diamond
Bos taurus	Q9N0K1	82.8%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
IFT57	protein-coding	55081
LINC01215	ncRNA	101929623
LINC00636	ncRNA	285205
LINC00635	ncRNA	151658

Protein

Protein identifiers

Leukocyte surface antigen CD47 — Q08722 (reviewed: Q08722)

Alternative names: Antigenic surface determinant protein OA3, Integrin-associated protein, Protein MER6

All UniProt accessions (5): A0A0A1TSG4, A0A2R8Y484, Q08722, H0YC40, H7BYS8

UniProt curated annotations — full annotation on UniProt →

Function. Adhesive protein that mediates cell-to-cell interactions. Acts as a receptor for thrombospondin THBS1 and as modulator of integrin signaling through the activation of heterotrimeric G proteins. Involved in signal transduction, cardiovascular homeostasis, inflammation, apoptosis, angiogenesis, cellular self-renewal, and immunoregulation. Plays a role in modulating pulmonary endothelin EDN1 signaling. Modulates nitrous oxide (NO) signaling, in response to THBS1, hence playing a role as a pressor agent, supporting blood pressure. Plays an important role in memory formation and synaptic plasticity in the hippocampus. Receptor for SIRPA, binding to which prevents maturation of immature dendritic cells and inhibits cytokine production by mature dendritic cells. Interaction with SIRPG mediates cell-cell adhesion, enhances superantigen-dependent T-cell-mediated proliferation and costimulates T-cell activation. Positively modulates FAS-dependent apoptosis in T-cells, perhaps by enhancing FAS clustering. Plays a role in suppressing angiogenesis and may be involved in metabolic dysregulation during normal aging. In response to THBS1, negatively modulates wound healing. Inhibits stem cell self-renewal, in response to THBS1, probably by regulation of the stem cell transcription factors POU5F1/OCT4, SOX2, MYC/c-Myc and KLF4. May play a role in membrane transport and/or integrin dependent signal transduction. May prevent premature elimination of red blood cells.

Subunit / interactions. Monomer. Interacts with THBS1 (via the C-terminal domain). Interacts with SIRPA. Interacts with FAS/CD95; interaction may be enhanced by functional activation. Interacts with SIRPG, UBQLN1 and UBQLN2. May interact with fibrinogen. Interacts with Aedes aegypti neutrophil-stimulating factor 1; the interaction results in inhibition of phagocytosis activity of macrophages.

Subcellular location. Cell membrane.

Tissue specificity. Very broadly distributed on normal adult tissues, as well as ovarian tumors, being especially abundant in some epithelia and the brain. Macrophages.

Induction. Induced in pulmonary artery and lung parenchyma following injury or stress. Expression in arteries increases in normal aging.

Isoforms (4)

UniProt ID	Names	Canonical?
Q08722-1	OA3-323	yes
Q08722-2	OA3-293
Q08722-3	OA3-305
Q08722-4	OA3-312

RefSeq proteins (3): NP_001369235, NP_001768, NP_942088 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006704	CD47	Family
IPR007110	Ig-like_dom	Domain
IPR013147	CD47-like_TM	Domain
IPR013270	CD47_Vset	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR037805	IgV_CD47	Domain

Pfam: PF04549, PF08204

UniProt features (52 total): strand 11, helix 11, topological domain 6, glycosylation site 6, transmembrane region 5, splice variant 4, modified residue 2, disulfide bond 2, turn 2, signal peptide 1, chain 1, domain 1

Structure

Experimental structures (PDB)

15 structures by resolution:

PDB	Title	Method	Resolution (Å)
2JJS	Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha	X-RAY DIFFRACTION	1.85
2VSC	Structure of the immunoglobulin-superfamily ectodomain of human CD47	X-RAY DIFFRACTION	1.9
4CMM	Structure of human CD47 in complex with human Signal Regulatory Protein (SIRP) alpha v1	X-RAY DIFFRACTION	1.92
4KJY	Complex of high-affinity SIRP alpha variant FD6 with CD47	X-RAY DIFFRACTION	1.93
8RP8	Structure of K2 Fab in complex with human CD47 ECD	X-RAY DIFFRACTION	2
5TZU	Crystal structure of human CD47 ECD bound to Fab of B6H12.2	X-RAY DIFFRACTION	2.1
2JJT	Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha	X-RAY DIFFRACTION	2.3
5TZ2	Crystal structure of human CD47 ECD bound to Fab of C47B222	X-RAY DIFFRACTION	2.3
8ZCA	Crystal structure of human CD47 ECD bound to Fab of Hu1C8	X-RAY DIFFRACTION	2.5
7XJF	Crystal structure of 6MW3211 Fab in complex with CD47	X-RAY DIFFRACTION	2.6
7YGG	Crystal structure of human CD47 in complex with engineered SIRPa.D1(N80A)	X-RAY DIFFRACTION	2.76
5IWL	CD47-diabody complex	X-RAY DIFFRACTION	2.8
7WN8	Crystal structure of antibody (BC31M5) binds to CD47	X-RAY DIFFRACTION	2.8
5TZT	Crystal structure of human CD47 ECD bound to Fab of C47B161	X-RAY DIFFRACTION	2.89
7MYZ	Structure of the full length 5-TM receptor CD47 bound to Fab B6H12	X-RAY DIFFRACTION	3.4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q08722-F1	86.48	0.67

Antibody-complex structures (SAbDab)

12 antibodies co-crystallized with this protein: 5IWL, 5TZ2, 5TZT, 5TZU, 7MYZ, 7WN8, 7XJF, 8RP8, 8ZCA, MAGROLIMAB, SAFIMESTOMIG, ZERIPATAMIG

Human Protein Atlas

Protein class: CD markers, Transporters, Transporter channels and pores, Predicted membrane proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): plasma membrane; vesicles

Antibody reliability (HPA): IH approved · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2)

Type	Positions
Pyrrolidone carboxylic acid	19
Phosphoserine	89

Disulfide bonds (2)

Type	Positions
Disulfide bond	33–263, 41–114

Glycosylation sites (6)

Type	Positions
N-linked (glcnac…) asparagine	23, 34, 50, 73, 111, 206

Function

Pathways and Gene Ontology

Reactome pathways

3 curated (TAS) of 9; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

9 pathways:

ID	Pathway	Evidence
R-HSA-202733	Cell surface interactions at the vascular wall	curated
R-HSA-216083	Integrin cell surface interactions	curated
R-HSA-6798695	Neutrophil degranulation	curated
R-HSA-1500931	Cell-Cell communication	—
R-HSA-1474244	Extracellular matrix organization	—
R-HSA-109582	Hemostasis	—
R-HSA-168256	Immune System	—
R-HSA-168249	Innate Immune System	—
R-HSA-391160	Signal regulatory protein family interactions	electronic

MSigDB gene sets: 504 (showing top): GGGACCA_MIR133A_MIR133B, GOBP_REGULATION_OF_CELL_ACTIVATION, FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP, GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, REACTOME_INNATE_IMMUNE_SYSTEM, BENPORATH_ES_WITH_H3K27ME3, MORF_MBD4, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, TGCGCANK_UNKNOWN, GOBP_MYELOID_LEUKOCYTE_MIGRATION, MORF_RAB5A, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, GOCC_SECRETORY_GRANULE, GCANCTGNY_MYOD_Q6

GO Biological Process (28): angiogenesis (GO:0001525), apoptotic process (GO:0006915), inflammatory response (GO:0006954), integrin-mediated signaling pathway (GO:0007229), positive regulation of cell population proliferation (GO:0008284), cell migration (GO:0016477), positive regulation of cell-cell adhesion (GO:0022409), regulation of type II interferon production (GO:0032649), regulation of interleukin-10 production (GO:0032653), regulation of interleukin-12 production (GO:0032655), regulation of interleukin-6 production (GO:0032675), regulation of tumor necrosis factor production (GO:0032680), regulation of nitric oxide biosynthetic process (GO:0045428), positive regulation of inflammatory response (GO:0050729), negative regulation of phagocytosis (GO:0050765), positive regulation of phagocytosis (GO:0050766), positive regulation of T cell activation (GO:0050870), positive regulation of stress fiber assembly (GO:0051496), regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368), cellular response to type II interferon (GO:0071346), cellular response to interleukin-1 (GO:0071347), cellular response to interleukin-12 (GO:0071349), ATP export (GO:1904669), positive regulation of monocyte extravasation (GO:2000439), positive regulation of immune system process (GO:0002684), cell adhesion (GO:0007155), heterotypic cell-cell adhesion (GO:0034113), cell-cell adhesion (GO:0098609)

GO Molecular Function (5): fibrinogen binding (GO:0070051), thrombospondin receptor activity (GO:0070053), protein binding involved in heterotypic cell-cell adhesion (GO:0086080), cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (5): plasma membrane (GO:0005886), cell surface (GO:0009986), specific granule membrane (GO:0035579), extracellular exosome (GO:0070062), tertiary granule membrane (GO:0070821)

Reactome top-level categories

5 top-level categories:

Category	Pathways
Hemostasis	1
Extracellular matrix organization	1
Cell-Cell communication	1
Innate Immune System	1
Immune System	1

GO top-level categories

57 GO namespaces:

Category	Terms
regulation of cytokine production	4
cell-cell adhesion	2
phagocytosis	2
regulation of phagocytosis	2
secretory granule membrane	2
blood vessel morphogenesis	1
anatomical structure formation involved in morphogenesis	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
defense response	1
cell surface receptor signaling pathway	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
cell motility	1
regulation of cell-cell adhesion	1
positive regulation of cell adhesion	1
type II interferon production	1
interleukin-10 production	1
interleukin-12 production	1
interleukin-6 production	1
tumor necrosis factor production	1
regulation of tumor necrosis factor superfamily cytokine production	1
nitric oxide biosynthetic process	1
regulation of biosynthetic process	1
regulation of nitric oxide metabolic process	1
inflammatory response	1
positive regulation of defense response	1
positive regulation of response to external stimulus	1
regulation of inflammatory response	1
negative regulation of endocytosis	1
positive regulation of endocytosis	1
T cell activation	1
regulation of T cell activation	1
positive regulation of lymphocyte activation	1
positive regulation of leukocyte cell-cell adhesion	1
positive regulation of actin filament bundle assembly	1
stress fiber assembly	1
regulation of stress fiber assembly	1
Fc receptor mediated stimulatory signaling pathway	1
regulation of signal transduction	1
regulation of immune response	1
response to type II interferon	1
cellular response to cytokine stimulus	1
protein-containing complex binding	1
signaling receptor activity	1
heterotypic cell-cell adhesion	1
cell-cell adhesion mediator activity	1
cell adhesion mediator activity	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1
specific granule	1
extracellular vesicle	1
tertiary granule	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 15 of 38 annotations. The rest are phylogenetic / computational / electronic (IEA).

15 experimentally-supported GO terms:

GO term	NS	Evidence
ATP export	BP	direct assay
cellular response to interleukin-12	BP	mutant phenotype
positive regulation of T cell activation	BP	direct assay
positive regulation of cell population proliferation	BP	direct assay
positive regulation of cell-cell adhesion	BP	direct assay
regulation of interleukin-10 production	BP	mutant phenotype
regulation of interleukin-12 production	BP	mutant phenotype
regulation of interleukin-6 production	BP	mutant phenotype
regulation of tumor necrosis factor production	BP	mutant phenotype
regulation of type II interferon production	BP	mutant phenotype
cell surface	CC	direct assay
plasma membrane	CC	direct assay
cell-cell adhesion mediator activity	MF	physical interaction
fibrinogen binding	MF	direct assay
thrombospondin receptor activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 2,708 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD47	SIRPA	P78324	971
CD47	SIRPG	Q9P1W8	881
CD47	RHAG	Q02094	873
CD47	THBS1	P07996	823
CD47	H3BT10	H3BT10	779
CD47	SIRPB1	O00241	774
CD47	CD274	Q9NZQ7	756
CD47	CALR	P27797	745
CD47	PRR13	Q9NZ81	733
CD47	MYC	P01106	704
CD47	SCARB1	Q8WTV0	690
CD47	GYPB	P06028	687
CD47	SCARB2	Q14108	684
CD47	CD36	P16671	684
CD47	CTLA4	P16410	680

IntAct

Human interaction partners of CD47 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

7 partners by confidence:

Partner	Interaction type	MIscore	Records
SIRPA	direct interaction	0.790	4
SIRPG	physical association	0.710	4
SYNE4	physical association	0.560	3
SIRPB1	direct interaction	0.440	1
HLA-C	physical association	0.400	1
TMEM243	physical association	0.400	1
ITGB1	association	0.350	1

BioGRID (93 interactions; top human partners by supporting records): LGALS9 (Affinity Capture-MS; 4 records), FAM134C (Affinity Capture-MS; 3 records), LGALS8 (Affinity Capture-MS; 3 records), SRC (Affinity Capture-Western; 3 records), TSPAN5 (Affinity Capture-MS; 3 records), BNIP3 (Two-hybrid; 2 records), BSCL2 (Affinity Capture-MS; 2 records), KLRG2 (Affinity Capture-MS; 2 records), LGALS9C (Affinity Capture-MS; 2 records), LILRB4 (Affinity Capture-MS; 2 records), S1PR1 (Affinity Capture-MS; 2 records), SLC1A5 (Affinity Capture-MS; 2 records), TM4SF18 (Affinity Capture-MS; 2 records), TRIM21 (Affinity Capture-MS; 2 records), AGPAT1 (Affinity Capture-MS)

SIGNOR signaling

2 signaling interactions:

A	Effect	B	Mechanism
CD47	“form complex”	“Ankyrin complex”	binding
THBS2	up-regulates	CD47	binding

Protein complexes (CORUM) (7)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

7 complexes by size:

Complex	Subunits	Members
★ ITGA2b-ITGB3-CD9-GP1b-CD47 complex	5	CD47, CD9, GP1BA, ITGA2B, ITGB3
★ ITGAV-ITGB3-CD47-FCER2 complex	4	CD47, FCER2, ITGAV, ITGB3
★ ITGA2b-ITGB3-CD47-SRC complex	4	CD47, ITGA2B, ITGB3, SRC
★ ITGA2B-ITGB3-CD47-FAK complex	4	ITGA2B, ITGB3, PTK2, CD47
★ ITGB3-ITGAV-CD47 complex	3	CD47, ITGAV, ITGB3
★ ITGA4-ITGB1-CD47 complex	3	CD47, ITGA4, ITGB1
★ ITGA2-ITGB1-CD47 complex	3	CD47, ITGA2, ITGB1

Ligand–receptor pairs (CellPhoneDB) (3)

Curated ligand–receptor partners (cell-cell communication), distinct from the protein–protein interactions above.

3 ligand–receptor pairs:

Partner	This gene’s role	Signaling class
SIRPB1;TYROBP	ligand
SIRPA	ligand
SIRPG	ligand

Disease & clinical

Genetic variants

Variant evidence for CD47: 63 ClinVar records (0 pathogenic / likely pathogenic); 7 GWAS associations.

ClinVar

63 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	0
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 918):

Position(s)	Effect	Δscore	Sites
3:108047132	donor_gain	1.0000
3:108059450–108059451	donor_loss	1.0000	5
3:108060854	acceptor_gain	1.0000
3:108054299	donor_gain	0.9900
3:108055512	donor_gain	0.9900
3:108058335–108058336	donor_loss	0.9900	6
3:108059545–108059547	acceptor_loss	0.9900	7
3:108059555	acceptor_loss	0.9900
3:108060743–108060744	donor_loss	0.9900	6
3:108060853–108060854	acceptor_loss	0.9900	5

AlphaMissense

850 missense substitutions predicted likely pathogenic (of 2,082 scored), across 232 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
F137	8	0.966	0.997
F313	8	0.910	0.985
N311	8	0.852	0.966
F22	8	0.844	0.978
F148	8	0.820	0.924
C114	7	0.997	0.999
C41	7	0.995	0.998
W58	7	0.994	0.999
C33	7	0.989	0.995
C263	7	0.982	0.991
W136	7	0.979	0.997
W157	7	0.954	0.999
F68	7	0.949	0.989
E307	7	0.943	0.973
E308	7	0.902	0.954
E122	7	0.876	0.917
N34	7	0.870	0.963
E118	7	0.870	0.964
F228	7	0.870	0.942
F156	7	0.861	0.973

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	1.03e-05
Lung Squamous Cell Carcinoma (TCGA)	unfavorable	9.98e-05
Thyroid Carcinoma (TCGA)	favorable	0.00042

Disease associations

OMIM: gene MIM:601028 | disease phenotypes:

GWAS associations

7 associations:

Study	Trait	p-value
GCST006922_10	Regular attendance at a religious group	8e-12
GCST010002_435	Refractive error	4e-10
GCST011102_6	Bipolar disorder	2e-9
GCST008103_182	Bipolar disorder	2e-8
GCST012465_51	Bipolar disorder	4e-8
GCST002783_603	Body mass index	2e-6
GCST002783_224	Body mass index	5e-6

EFO canonical traits (from GWAS)

2 canonical traits:

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0009592	social interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3714583 (SINGLE PROTEIN)

Drugs by curated mechanism of action (ChEMBL)

Drugs whose curated ChEMBL mechanism of action targets the CD47 protein itself — single-protein targets only (drugs acting on a protein family or complex that merely includes it are excluded). Includes antibodies and oligonucleotides that bioactivity screening does not capture.

2 curated-mechanism drugs:

Drug	Modality	Max phase
MAGROLIMAB	Antibody	3
EVORPACEPT	Protein	2

PharmGKB: 1 entry (CPIC guideline: no)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — CD molecules

Most potent curated ligand interactions (4 total), top 4:

Ligand	Action	Affinity	Parameter
magrolimab	Binding	11.1	pKd
ligufalimab	Binding	9.49	pEC50
evorpacept	Binding	9.0	pKd
ontorpacept	Binding	7.85	pEC50

Binding affinities (BindingDB)

20 measured of 20 human assays (20 total across all organisms); most potent 20 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL4522427	KD	190 nM
CHEMBL3891508	KD	1200 nM
CHEMBL3946082	KD	1500 nM
CHEMBL3971661	KD	3040 nM
CHEMBL3900522	KD	6200 nM
CHEMBL4474790	KD	8600 nM
CHEMBL4462459	KD	9500 nM
CHEMBL3975422	KD	10000 nM
CHEMBL4570565	KD	13000 nM
CHEMBL4462869	KD	15000 nM
CHEMBL4585124	KD	17000 nM
CHEMBL3911226	KD	18000 nM
CHEMBL3974452	KD	19000 nM
CHEMBL4573126	KD	20000 nM
CHEMBL4449880	KD	21000 nM
CHEMBL3939184	KD	27000 nM
CHEMBL4471112	KD	36000 nM
CHEMBL4470419	KD	38000 nM
CHEMBL3899400	KD	42000 nM
CHEMBL4545895	KD	48000 nM

ChEMBL bioactivities

10 potent at pChembl≥5 of 25 total, top 10 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.72	Kd	190	nM	CHEMBL4522427
6.11	Kd	771	nM	CHEMBL3946082
5.92	Kd	1200	nM	CHEMBL3891508
5.82	Kd	1500	nM	CHEMBL3946082
5.64	Kd	2280	nM	CHEMBL3974452
5.52	Kd	3040	nM	CHEMBL3971661
5.21	Kd	6200	nM	CHEMBL3900522
5.07	Kd	8600	nM	CHEMBL4474790
5.02	Kd	9500	nM	CHEMBL4462459
5.00	Kd	1e+04	nM	CHEMBL3975422

PubChem BioAssay actives

10 with measured affinity, of 31 total; 9 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(2R)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R)-6-amino-2-[5-[4-[[bis[[1-[5-[[(2R)-6-amino-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-6-amino-1-[[(1R)-5-amino-1-carboxypentyl]amino]-1-oxohexan-2-yl]amino]-3-(1H-indol-3-yl)-1-oxopropan-2-yl]amino]-1-oxohexan-2-yl]amino]-3-methyl-1-oxobutan-2-yl]amino]-3-methyl-1-oxobutan-2-yl]amino]-3-(4-hydroxyphenyl)-1-oxopropan-2-yl]amino]-1-oxo-3-phenylpropan-2-yl]amino]-5-carbamimidamido-1-oxopentan-2-yl]-methylamino]-1-oxohexan-2-yl]amino]-5-oxopentyl]triazol-4-yl]methyl]amino]methyl]triazol-1-yl]pentanoylamino]hexanoyl]-methylamino]-5-carbamimidamidopentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]hexanoyl]amino]-3-(1H-indol-3-yl)propyl]amino]hexanoyl]amino]hexanoic acid	1615551: Binding affinity to CD47 in biotinylated human MEC1 cell membranes by biolayer interferometry	kd	0.1900	uM
(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-acetamido-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-4-methylsulfanylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-6-aminohexanamide	1316205: Binding affinity to CD47 receptor in human NT.115-labeled MEC1 cell membranes after 5 mins by MST assay	kd	0.7710	uM
(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-acetamido-6-aminohexanoyl]amino]-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-4-methylsulfanylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-6-aminohexanoyl]amino]-6-aminohexanamide	1316205: Binding affinity to CD47 receptor in human NT.115-labeled MEC1 cell membranes after 5 mins by MST assay	kd	1.2000	uM
(2S)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2,6-diaminohexanoyl]amino]-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-4-methylsulfanylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]hexanoyl]amino]hexanoic acid	1316205: Binding affinity to CD47 receptor in human NT.115-labeled MEC1 cell membranes after 5 mins by MST assay	kd	2.2800	uM
(2R)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R)-2,6-diaminohexanoyl]amino]-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-4-methylsulfanylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]hexanoyl]amino]hexanoic acid	1316205: Binding affinity to CD47 receptor in human NT.115-labeled MEC1 cell membranes after 5 mins by MST assay	kd	3.0400	uM
(2R)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R)-2,6-diaminohexanoyl]amino]propanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-4-methylsulfanylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]hexanoyl]amino]hexanoic acid	1316206: Binding affinity to CD47 receptor in human biotinylated MEC1 cell membranes by biolayer interferometry	kd	6.2000	uM
(2R)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R)-2,6-diaminohexanoyl]-methylamino]-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]hexanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]hexanoyl]amino]hexanoic acid	1615551: Binding affinity to CD47 in biotinylated human MEC1 cell membranes by biolayer interferometry	kd	8.6000	uM
(2R)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R)-2,6-diaminohexanoyl]-methylamino]-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]hexanoyl]amino]hexanoic acid	1615551: Binding affinity to CD47 in biotinylated human MEC1 cell membranes by biolayer interferometry	kd	9.5000	uM
(2S)-6-amino-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-amino-5-(diaminomethylideneamino)pentanoyl]amino]-3-phenylpropanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]-3-methylbutanoyl]amino]-3-methylbutanoyl]amino]-4-methylsulfanylbutanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]hexanoic acid	1316205: Binding affinity to CD47 receptor in human NT.115-labeled MEC1 cell membranes after 5 mins by MST assay	kd	10.0000	uM

CTD chemical–gene interactions

71 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression, affects expression, decreases methylation	9
Air Pollutants	increases abundance, increases expression, affects expression, decreases expression, affects cotreatment	4
Tetrachlorodibenzodioxin	decreases expression, decreases reaction, increases expression	3
Tobacco Smoke Pollution	decreases expression, affects expression	3
sodium arsenite	affects cotreatment, decreases expression, increases abundance	2
Arsenic	affects cotreatment, decreases expression, increases abundance	2
Vehicle Emissions	decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation, increases expression	2
Copper	increases expression, decreases expression, affects binding	2
Nickel	increases expression	2
Ozone	affects cotreatment, increases expression, increases abundance, affects expression	2
Smoke	decreases expression, increases abundance	2
Particulate Matter	decreases expression, increases abundance	2
bisphenol F	increases expression	1
beauvericin	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
propionaldehyde	increases expression	1
bisphenol A	increases expression	1
senecionine	increases expression	1
terbufos	decreases methylation	1
trichostatin A	increases expression	1
methylparaben	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	increases expression	1
4-hydroxy-2-nonenal	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
enniatins	affects cotreatment, increases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3855090	Binding	Binding affinity to CD47 receptor in human NT.115-labeled MEC1 cell membranes after 5 mins by MST assay	Thrombospondin-1 Mimetic Agonist Peptides Induce Selective Death in Tumor Cells: Design, Synthesis, and Structure-Activity Relationship Studies. — *J Med Chem*

Cellosaurus cell lines

16 cell lines: 10 cancer cell line, 4 spontaneously immortalized cell line, 2 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2TU	Abcam HEK293T CD47 KO	Transformed cell line	Female
CVCL_D7M6	Ubigene A-549 CD47 KO	Cancer cell line	Male
CVCL_D8IP	Ubigene HCT 116 CD47 KO	Cancer cell line	Male
CVCL_D9ZN	Ubigene HeLa CD47 KO	Cancer cell line	Female
CVCL_E1G9	Abcam MCF-7 CD47 KO	Cancer cell line	Female
CVCL_E6BK	MC38-hPD-L1-hCD47-LZ	Cancer cell line	Female
CVCL_E6PN	Genomeditech CHO-K1 H_CD47	Spontaneously immortalized cell line	Female
CVCL_E6PP	Genomeditech CHO-K1 H_CD47 aAPC	Spontaneously immortalized cell line	Female
CVCL_E6WD	Genomeditech MC-38 H_CD47	Cancer cell line	Female
CVCL_E8IT	Jurkat-NFAT-Luc2-CD47-KO-1B3	Cancer cell line	Male

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for CD47 across ~30M SureChEMBL compounds — explore on Sugi Predict.