AMD1

gene
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Also known as SAMDC

Summary

AMD1 (adenosylmethionine decarboxylase 1, HGNC:457) is a protein-coding gene on chromosome 6q21, encoding S-adenosylmethionine decarboxylase proenzyme (P17707). Essential for biosynthesis of the polyamines spermidine and spermine. It is a selective cancer dependency (DepMap: 43.0% of cell lines).

This gene encodes an important intermediate enzyme in polyamine biosynthesis. The polyamines spermine, spermidine, and putrescine are low-molecular-weight aliphatic amines essential for cellular proliferation and tumor promotion. Multiple alternatively spliced transcript variants have been identified. Pseudogenes of this gene are found on chromosomes 5, 6, 10, X and Y.

Source: NCBI Gene 262 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 60 total — 2 pathogenic, 1 likely-pathogenic
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 43.0% of screened cell lines
  • MANE Select transcript: NM_001634

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:457
Approved symbolAMD1
Nameadenosylmethionine decarboxylase 1
Location6q21
Locus typegene with protein product
StatusApproved
AliasesSAMDC
Ensembl geneENSG00000123505
Ensembl biotypeprotein_coding
OMIM180980
Entrez262

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000368876, ENST00000368877, ENST00000368885, ENST00000451850, ENST00000465404, ENST00000612642, ENST00000619590, ENST00000672937, ENST00000675380, ENST00000851729, ENST00000940236, ENST00000940237, ENST00000940238, ENST00000940239, ENST00000940240

RefSeq mRNA: 7 — MANE Select: NM_001634 NM_001287214, NM_001287215, NM_001287216, NM_001393406, NM_001393407, NM_001393408, NM_001634

CCDS: CCDS5086, CCDS75504, CCDS75505

Canonical transcript exons

ENST00000368885 — 9 exons

ExonStartEnd
ENSE00002270479110890254110890356
ENSE00003443472110893476110895713
ENSE00003525544110888857110888983
ENSE00003566640110892161110892203
ENSE00003568309110887505110887591
ENSE00003714051110892735110892827
ENSE00003742253110892299110892443
ENSE00003746288110892910110893065
ENSE00003844320110874785110875215

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 110.6608 / max 1085.8300, expressed in 1824 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
69262108.77441824
692581.2819720
692590.4477205
692600.087730
2041500.069029

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.24gold quality
oocyteCL:000002398.73gold quality
corpus callosumUBERON:000233697.95gold quality
prostate glandUBERON:000236797.74gold quality
mucosa of sigmoid colonUBERON:000499396.93gold quality
middle frontal gyrusUBERON:000270296.54gold quality
C1 segment of cervical spinal cordUBERON:000646996.48gold quality
postcentral gyrusUBERON:000258196.22gold quality
colonic mucosaUBERON:000031796.12gold quality
oral cavityUBERON:000016796.07gold quality
medial globus pallidusUBERON:000247795.98gold quality
spinal cordUBERON:000224095.95gold quality
heart right ventricleUBERON:000208095.90gold quality
esophagus squamous epitheliumUBERON:000692095.81gold quality
parietal lobeUBERON:000187295.76gold quality
amniotic fluidUBERON:000017395.73gold quality
globus pallidusUBERON:000187595.69gold quality
endometriumUBERON:000129595.66gold quality
monocyteCL:000057695.59gold quality
choroid plexus epitheliumUBERON:000391195.53gold quality
prefrontal cortexUBERON:000045195.48gold quality
mononuclear cellCL:000084295.39gold quality
inferior vagus X ganglionUBERON:000536395.32gold quality
lower lobe of lungUBERON:000894995.31gold quality
leukocyteCL:000073895.28gold quality
Ammon’s hornUBERON:000195495.16gold quality
bone marrowUBERON:000237195.06gold quality
epithelium of esophagusUBERON:000197695.00gold quality
cauda epididymisUBERON:000436094.94gold quality
palpebral conjunctivaUBERON:000181294.93gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-135922yes19.89
E-HCAD-1yes11.43
E-ENAD-20no1253.52
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

191 targeting AMD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-4533100.0069.482758
HSA-MIR-453199.9969.703181
HSA-MIR-186-5P99.9970.833707
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-569699.9872.364487
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548N99.9871.944170
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-9983-3P99.9471.483631

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 43.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 21)

  • AdoMetDC is ubiquitinated and degraded by the 26 S proteasome (PMID:14718534)
  • The adhesion-dependent expression of SAM-DC and ODC contributes to extracellular matrix-dependent salivary gland cell differentiation. (PMID:15521072)
  • For such cells, gamma-radiation and cisplatin, which are direct DNA-damaging agents, were very effective for promoting cell death. (PMID:17069747)
  • schizophrenia and bipolar disorder patients, the increase of S-adenosyl methionine is associated with an overexpression of DNA methyltransferase-1 mRNA in Brodmann’s area 9 GABAergic neurons. (PMID:17259861)
  • Antisense RNA specifically inhibited the expression of ODC and AdoMetDC and the synthesis of polyamine, while it induced p21 expression, resulting in cell growth arrest in the G1 phase in prostate cancer cells (PMID:18548481)
  • Binding of putrescine to wild type dimeric ADOMETDC protein is cooperative; putrescine activates the enzyme through electrostatic effects and acts as a switch to correctly orient key catalytic residues. (PMID:19053272)
  • determined crystal structures cocrystallized with 5’-deoxy-5’-dimethylthioadenosine and 5’-deoxy-5’-(N-dimethyl)amino-8-methyladenosine. The crystal structures revealed cation-pi interaction between the ligand and aromatic side chains of Phe7 and Phe223 (PMID:19527050)
  • Decreased AMD1 is associated with prostate cancer. (PMID:20215859)
  • Overexpression of S-adenosylmethionine decarboxylase in rodent fibroblasts led to aggressive transformants. (PMID:21134486)
  • This study demomistrated that H3K4me3 modification plays an important role in up regulation of AMD1 in prefrontal cortex. (PMID:22008221)
  • Genetic variant of AMD1 is associated with obesity. (PMID:22496743)
  • Gene expression studies have identified altered expression of AMD1 in suicide completers with a history of mood disorders. (PMID:23260169)
  • (AMD1)-mediated mRNA processing and cell adhesion activated & inhibited transition mechanisms (PMID:24652003)
  • AMD1 gene variants previously found to associate among Indian children did not associate with risk of obesity or obesity-related quantitative measures among Caucasian children and juvenile men from Denmark. (PMID:26558825)
  • AMD1 is upregulated in human prostate cancer with activated mTORC1 (PMID:28658205)
  • AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation (PMID:29310120)
  • this study shows that AMD1 promotes cell migration in epidermal wound healimg (PMID:29906410)
  • Three SNPs (RUNX3 rs7553295 G > T, AMD1 rs1279590 G > A and MSRA rs73534533 C > A) were replicated in the validation dataset, and their meta-analysis showed an adjusted hazards ratio [HR] of 0.82 [95% confidence interval (CI) =0.75-0.89] and pmeta = 2.86 x 10(-6) , 0.81 (0.73-0.91) and pmeta = 4.63 x 10(-4) , and 0.77 (0.68-0.89) and pmeta = 2.07 x 10(-4) , respectively). (PMID:30650190)
  • Polyamine synthesis enzyme AMD1 is closely associated with tumorigenesis and prognosis of human gastric cancers. (PMID:31140554)
  • AMD1 is required for the maintenance of leukemic stem cells and promotes chronic myeloid leukemic growth. (PMID:33203990)
  • AMD1 promotes breast cancer aggressiveness via a spermidine-eIF5A hypusination-TCF4 axis. (PMID:38654332)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioamd1ENSDARG00000043856
mus_musculusAmd2ENSMUSG00000063953
mus_musculusAmd1ENSMUSG00000075232
rattus_norvegicusAmd1ENSRNOG00000000585
drosophila_melanogasterSamDCFBGN0019932
caenorhabditis_eleganssmd-1WBGENE00004875

Protein

Protein identifiers

S-adenosylmethionine decarboxylase proenzymeP17707 (reviewed: P17707)

All UniProt accessions (5): A0A5F9ZHD5, B4DZ60, F6R5I9, P17707, Q5VXN5

UniProt curated annotations — full annotation on UniProt →

Function. Essential for biosynthesis of the polyamines spermidine and spermine. Promotes maintenance and self-renewal of embryonic stem cells, by maintaining spermine levels.

Subunit / interactions. Heterotetramer of two alpha and two beta chains.

Post-translational modifications. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain.

Activity regulation. Both proenzyme processing and catalytic activity are stimulated by putrescine. Catalytic activity is inhibited by iodoacetic acid.

Cofactor. Binds 1 pyruvoyl group covalently per subunit.

Pathway. Amine and polyamine biosynthesis; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine from S-adenosyl-L-methionine: step 1/1.

Similarity. Belongs to the eukaryotic AdoMetDC family.

Isoforms (2)

UniProt IDNamesCanonical?
P17707-11yes
P17707-22

RefSeq proteins (7): NP_001274143, NP_001274144, NP_001274145, NP_001380335, NP_001380336, NP_001380337, NP_001625* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001985S-AdoMet_decarboxylase_eukFamily
IPR016067S-AdoMet_deCO2ase_coreHomologous_superfamily
IPR018166S-AdoMet_deCO2ase_CSConserved_site
IPR048283AdoMetDC-likeFamily

Pfam: PF01536

Enzyme classification (BRENDA):

  • EC 4.1.1.50 — adenosylmethionine decarboxylase (BRENDA: 59 organisms, 25 substrates, 228 inhibitors, 45 Km, 15 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
S-ADENOSYL-L-METHIONINE0.0019–136
S-ADENOSYLMETHIONINE0.06–0.964
LYSINE1.5181
S-ADENOSYL-METHIONINE0

Catalyzed reactions (Rhea), 1 shown:

  • S-adenosyl-L-methionine + H(+) = S-adenosyl 3-(methylsulfanyl)propylamine + CO2 (RHEA:15981)

UniProt features (73 total): mutagenesis site 25, strand 17, helix 13, active site 6, binding site 4, chain 2, modified residue 2, site 1, splice variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

28 structures.

PDBMethodResolution (Å)
1JL0X-RAY DIFFRACTION1.5
3EP6X-RAY DIFFRACTION1.7
1MSVX-RAY DIFFRACTION1.75
3EPBX-RAY DIFFRACTION1.75
3H0WX-RAY DIFFRACTION1.81
9P1HX-RAY DIFFRACTION1.81
3DZ6X-RAY DIFFRACTION1.83
3DZ4X-RAY DIFFRACTION1.84
3EP3X-RAY DIFFRACTION1.84
3DZ2X-RAY DIFFRACTION1.86
3EP4X-RAY DIFFRACTION1.89
1I7BX-RAY DIFFRACTION1.9
3DZ7X-RAY DIFFRACTION1.91
3EP8X-RAY DIFFRACTION1.97
3EP5X-RAY DIFFRACTION1.99
1I72X-RAY DIFFRACTION2
3EP7X-RAY DIFFRACTION2
1I79X-RAY DIFFRACTION2.01
3EPAX-RAY DIFFRACTION2.1
9PBBX-RAY DIFFRACTION2.17
9P7QX-RAY DIFFRACTION2.21
1I7MX-RAY DIFFRACTION2.24
3H0VX-RAY DIFFRACTION2.24
1JENX-RAY DIFFRACTION2.25
3EP9X-RAY DIFFRACTION2.35
1I7CX-RAY DIFFRACTION2.4
3DZ5X-RAY DIFFRACTION2.43
3DZ3X-RAY DIFFRACTION2.62

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P17707-F193.520.86

Functional residue map

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

Catalytic / active sites (7): 67–68 (cleavage (non-hydrolytic); by autolysis); 8; 11; 68 (schiff-base intermediate with substrate; via pyruvic acid); 82 (proton donor; for catalytic activity); 229 (proton acceptor; for processing activity); 243 (proton acceptor; for processing activity)

Ligand- & substrate-binding residues (4): 223; 247; 7; 67

Post-translational modifications (2): 68, 298

Mutagenesis-validated functional residues (25):

PositionPhenotype
7no effect.
8loss of activity. normal putrescine-stimulated processing.
11loss of activity. loss of putrescine-stimulated processing.
15little effect.
49little effect.
5017 percent decrease in catalytic activity. no effect on processing.
61little effect.
6638 percent decrease in catalytic activity. slight reduction in processing.
67little effect.
68–69loss of catalytic activity and processing.
68loss of catalytic activity and processing.
6924 percent decrease in catalytic activity. slight reduction in processing.
80greatly reduced catalytic activity. no putrescine-stimulated processing.
82loss of activity. greatly reduced putrescine-stimulated processing.
223no effect.
226little effect.
229loss of processing.
229greatly reduced processing.
229greatly reduced catalytic activity but little effect on processing.
243greatly reduced catalytic activity and processing.
243loss of processing.
247little effect.
249little effect.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-351202Metabolism of polyamines

MSigDB gene sets: 283 (showing top): MYAATNNNNNNNGGC_UNKNOWN, ELVIDGE_HYPOXIA_DN, AAGCAAT_MIR137, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GRUETZMANN_PANCREATIC_CANCER_DN, KAAB_FAILED_HEART_ATRIUM_DN, PAL_PRMT5_TARGETS_UP, BROWNE_HCMV_INFECTION_8HR_UP, ENK_UV_RESPONSE_KERATINOCYTE_UP, KEGG_CYSTEINE_AND_METHIONINE_METABOLISM, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, TATTATA_MIR374, GENTILE_RESPONSE_CLUSTER_D3, RACCACAR_AML_Q6, CHANDRAN_METASTASIS_DN

GO Biological Process (4): polyamine metabolic process (GO:0006595), spermine biosynthetic process (GO:0006597), spermidine biosynthetic process (GO:0008295), polyamine biosynthetic process (GO:0006596)

GO Molecular Function (6): adenosylmethionine decarboxylase activity (GO:0004014), putrescine binding (GO:0019810), identical protein binding (GO:0042802), protein binding (GO:0005515), lyase activity (GO:0016829), carboxy-lyase activity (GO:0016831)

GO Cellular Component (1): cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of amino acids and derivatives1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
polyamine biosynthetic process2
biogenic amine metabolic process1
spermine metabolic process1
spermidine metabolic process1
polyamine metabolic process1
biogenic amine biosynthetic process1
carboxy-lyase activity1
polyamine binding1
cation binding1
protein binding1
binding1
catalytic activity1
carbon-carbon lyase activity1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

72 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:0914”(association)0.900
MED28MED19psi-mi:“MI:0914”(association)0.730
SHC1AP2A1psi-mi:“MI:0914”(association)0.730
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
HDAC11CLUHpsi-mi:“MI:0914”(association)0.640
PTH2AMD1psi-mi:“MI:0915”(physical association)0.590
AMD1AMD1psi-mi:“MI:0915”(physical association)0.560
AMD1THAP4psi-mi:“MI:0915”(physical association)0.560
KPTNEIF4G3psi-mi:“MI:0914”(association)0.530
POP4NME2P1psi-mi:“MI:0914”(association)0.530
BMP15AMD1psi-mi:“MI:0914”(association)0.530
POMCAMD1psi-mi:“MI:0914”(association)0.530
PRELPAMD1psi-mi:“MI:0914”(association)0.530
GLTPAMD1psi-mi:“MI:0914”(association)0.530
FBXO4AMD1psi-mi:“MI:0914”(association)0.530
ARID1AACTL6Apsi-mi:“MI:0914”(association)0.530
CLEC11AVWA8psi-mi:“MI:0914”(association)0.530
MISPOBSL1psi-mi:“MI:0914”(association)0.530
ADCYAP1GGPS1psi-mi:“MI:0914”(association)0.530
RPP25LRPP40psi-mi:“MI:0914”(association)0.530

BioGRID (101): AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), AMD1 (Two-hybrid), AMD1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS)

ESM2 similar proteins: A1L4T4, A2XCT8, A2Z7C4, A9SCJ6, A9SDW6, A9SS00, B4G0F3, B7PRF6, B8BKI7, B9SQI7, C3ZAH2, C5WWY0, C5X1F5, D7T737, F6HDT7, F6QS54, F7FKV1, O00763, O48707, P17707, P28918, P35574, P46952, P46953, P50243, Q0VCA8, Q10RE5, Q2LZI9, Q2PQH8, Q3B8C8, Q3ZBL1, Q562C9, Q5IH13, Q5IH14, Q5ZL43, Q6DIY2, Q6DIZ0, Q6P7I0, Q6PBX5, Q6YXW6

Diamond homologs: A2XV58, D3Z6H8, O02655, O04009, O24575, O49972, O65354, O76240, O80402, P0DMN7, P17707, P17708, P21182, P28918, P46255, P50243, P50244, P79888, P82185, P91931, Q04694, Q0JC10, Q25264, Q27883, Q38IY3, Q39676, Q39677, Q3E9D5, Q42613, Q42679, Q42829, Q43820, Q8T1E3, Q96286, Q96471, Q96555, Q9AXE3, Q9LSU6, Q9M4D8, Q9M6K1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic1
Uncertain significance34
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
688010GRCh37/hg19 6q21-22.31(chr6:110981075-119608396)x1Pathogenic
973822NM_015076.5(CDK19):c.82G>C (p.Gly28Arg)Pathogenic
973825NM_015076.5(CDK19):c.83G>C (p.Gly28Ala)Likely pathogenic

SpliceAI

1096 predictions. Top by Δscore:

VariantEffectΔscore
6:110887588:TCAGG:Tdonor_loss1.0000
6:110887589:CAGG:Cdonor_loss1.0000
6:110887590:AGGTA:Adonor_loss1.0000
6:110887591:GGTAA:Gdonor_loss1.0000
6:110887592:G:Cdonor_loss1.0000
6:110887593:TAAGT:Tdonor_loss1.0000
6:110888849:A:AGacceptor_gain1.0000
6:110888852:T:Aacceptor_gain1.0000
6:110888855:A:AGacceptor_gain1.0000
6:110888855:AGT:Aacceptor_gain1.0000
6:110888856:G:GTacceptor_gain1.0000
6:110888856:GT:Gacceptor_gain1.0000
6:110888856:GTG:Gacceptor_gain1.0000
6:110888856:GTGA:Gacceptor_gain1.0000
6:110888983:AG:Adonor_loss1.0000
6:110888984:G:Adonor_loss1.0000
6:110888984:G:GGdonor_gain1.0000
6:110888985:T:Gdonor_loss1.0000
6:110890247:A:AGacceptor_gain1.0000
6:110890250:A:AGacceptor_gain1.0000
6:110890251:A:Gacceptor_gain1.0000
6:110890272:A:AGacceptor_gain1.0000
6:110890273:A:Gacceptor_gain1.0000
6:110890323:G:GTdonor_gain1.0000
6:110890357:G:GGdonor_gain1.0000
6:110892295:TTAG:Tacceptor_loss1.0000
6:110892298:G:GAacceptor_loss1.0000
6:110892298:GGT:Gacceptor_gain1.0000
6:110892432:G:GTdonor_gain1.0000
6:110892439:CTCGT:Cdonor_gain1.0000

AlphaMissense

2249 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:110875130:G:AG9R1.000
6:110875130:G:CG9R1.000
6:110875130:G:TG9W1.000
6:110875137:A:TE11V1.000
6:110875138:G:CE11D1.000
6:110875138:G:TE11D1.000
6:110875143:T:CL13P1.000
6:110875158:T:CF18S1.000
6:110887512:T:AW40R1.000
6:110887512:T:CW40R1.000
6:110887525:T:GL44W1.000
6:110887540:G:AC49Y1.000
6:110887541:T:GC49W1.000
6:110887578:G:CA62P1.000
6:110887581:T:GY63D1.000
6:110887588:T:AL65H1.000
6:110887588:T:CL65P1.000
6:110888859:A:TE67V1.000
6:110888861:A:CS68R1.000
6:110888862:G:TS68I1.000
6:110888863:T:AS68R1.000
6:110888863:T:GS68R1.000
6:110888864:A:CS69R1.000
6:110888865:G:TS69I1.000
6:110888866:C:AS69R1.000
6:110888866:C:GS69R1.000
6:110888870:T:CF71L1.000
6:110888871:T:CF71S1.000
6:110888871:T:GF71C1.000
6:110888872:T:AF71L1.000

dbSNP variants (sampled 300 via entrez): RS1000063460 (6:110843775 G>A,T), RS1000068511 (6:110884913 C>G), RS1000068626 (6:110813041 G>A), RS1000077249 (6:110882252 T>G), RS1000077809 (6:110823937 G>A), RS1000126302 (6:110882128 T>A), RS1000183600 (6:110860304 C>T), RS1000282289 (6:110887796 C>A,T), RS1000282424 (6:110817598 GA>G), RS1000314835 (6:110844405 G>A), RS1000367079 (6:110844597 C>G,T), RS1000370966 (6:110847312 T>G), RS1000376782 (6:110893850 C>T), RS1000421474 (6:110837606 G>T), RS1000437870 (6:110853561 C>A)

Disease associations

OMIM: gene MIM:180980 | disease phenotypes: MIM:618916

GenCC curated gene-disease

Mondo (1): developmental and epileptic encephalopathy, 87 (MONDO:0030059)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST006879_15Blood metabolite levels6.000000e-25
GCST006879_16Blood metabolite levels5.000000e-08
GCST006879_17Blood metabolite levels2.000000e-26
GCST006879_23Blood metabolite levels7.000000e-31
GCST006879_24Blood metabolite levels3.000000e-25
GCST006879_3Blood metabolite levels8.000000e-29
GCST006879_4Blood metabolite levels7.000000e-37

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4181 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — Decarboxylases

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
sardomozideInhibition8.0pIC50

Binding affinities (BindingDB)

24 measured of 34 human assays (34 total across all organisms); most potent 24 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
(2R,3R,4S,5R)-2-(6-amino-8-methyl-9H-purin-9-yl)-5-({4-(aminooxy)butylamino}methyl)oxolane-3,4-diolIC505 nM
(2R,3R,4S,5R)-2-(6-amino-8-methyl-9H-purin-9-yl)-5-({2-(aminooxy)ethylamino}methyl)oxolane-3,4-diolIC507 nM
(2R,3R,4S,5R)-2-(6-amino-8-hydroxy-9H-purin-9-yl)-5-({4-(aminooxy)butylamino}methyl)oxolane-3,4-diolIC5011 nM
(2R,3R,4S,5R)-2-(6-amino-8-ethyl-9H-purin-9-yl)-5-({4-(aminooxy)butylamino}methyl)oxolane-3,4-diolIC5015 nM
(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-({4-(aminooxy)butylamino}methyl)oxolane-3,4-diolIC5018 nM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)-9H-purin-9-yl]-5-({4-(aminooxy)butylamino}methyl)oxolane-3,4-diolIC5049 nM
(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-({2-(aminooxy)ethylamino}methyl)oxolane-3,4-diolIC5055 nM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)-9H-purin-9-yl]-5-({2-(aminooxy)ethylamino}methyl)oxolane-3,4-diolIC5086 nM
3-({[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)propanehydrazideIC50170 nM
3-({[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)propanamideIC50400 nM
(2R,3R,4S,5R)-2-(6-amino-8-methyl-9H-purin-9-yl)-5-[(dimethylamino)methyl]oxolane-3,4-diolIC50600 nM
3-({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)propanehydrazideIC501500 nM
{[(2S,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}dimethylsulfanium chlorideIC503000 nM
3-({[(2R,3S,4R,5R)-5-(6-amino-8-ethyl-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)propanamideIC504000 nM
3-({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)propanamideIC507000 nM
(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-[(dimethylamino)methyl]oxolane-3,4-diolIC509000 nM
{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}dimethylsulfanium chlorideIC5015000 nM
2-({[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)acetohydrazideIC5031000 nM
(2R,3R,4S,5R)-2-(6-amino-8-methyl-9H-purin-9-yl)-5-{[(3-aminopropyl)(methyl)amino]methyl}oxolane-3,4-diolIC5070000 nM
(2R,3R,4S,5R)-2-(6-amino-8-methyl-9H-purin-9-yl)-5-{[(2-aminoethyl)(methyl)amino]methyl}oxolane-3,4-diolIC5088000 nM
3-({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(methyl)amino)-N’-hydroxypropanimidamideIC50157000 nM
(2R,3R,4S,5R)-2-(6-amino-8-ethyl-9H-purin-9-yl)-5-{[(3-aminopropyl)(methyl)amino]methyl}oxolane-3,4-diolIC50420000 nM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)-9H-purin-9-yl]-5-{[(3-aminopropyl)(methyl)amino]methyl}oxolane-3,4-diolIC50440000 nM
(2R,3R,4S,5R)-2-(6-amino-9H-purin-9-yl)-5-{[(3-aminopropyl)(methyl)amino]methyl}oxolane-3,4-diolIC50500000 nM

ChEMBL bioactivities

21 potent at pChembl≥5 of 38 total, top 20 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.30IC505nMCHEMBL517131
8.15IC507nMCHEMBL510356
7.96IC5011nMCHEMBL461970
7.82IC5015nMCHEMBL461779
7.75IC5018nMCHEMBL516811
7.31IC5049nMCHEMBL460719
7.26IC5055nMCHEMBL461780
7.07IC5086nMCHEMBL453372
6.77IC50170nMCHEMBL517593
6.40IC50400nMCHEMBL462656
6.22IC50600nMCHEMBL516214
5.82IC501500nMCHEMBL462138
5.52IC503000nMCHEMBL473134
5.42Ki3800nMCHEMBL2115571
5.40IC504000nMCHEMBL517908
5.30IC505000nMCHEMBL473336
5.16IC507000nMCHEMBL461969
5.14Ki7200nMCHEMBL3392185
5.05IC509000nMCHEMBL472733
5.05IC509000nMCHEMBL3392189

PubChem BioAssay actives

33 with measured affinity, of 218 total; 26 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
(2R,3R,4S,5R)-2-(6-amino-8-methylpurin-9-yl)-5-[[4-aminooxybutyl(methyl)amino]methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0050uM
(2R,3R,4S,5R)-2-(6-amino-8-methylpurin-9-yl)-5-[[4-aminooxybutyl(methyl)amino]methyl]oxolane-3,4-diol;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0050uM
(2R,3R,4S,5R)-2-(6-amino-8-methylpurin-9-yl)-5-[[2-aminooxyethyl(methyl)amino]methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0070uM
(2R,3R,4S,5R)-2-(6-amino-8-methylpurin-9-yl)-5-[[2-aminooxyethyl(methyl)amino]methyl]oxolane-3,4-diol;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0070uM
6-amino-9-[(2R,3R,4S,5R)-5-[[4-aminooxybutyl(methyl)amino]methyl]-3,4-dihydroxyoxolan-2-yl]-7H-purin-8-one1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0110uM
6-amino-9-[(2R,3R,4S,5R)-5-[[4-aminooxybutyl(methyl)amino]methyl]-3,4-dihydroxyoxolan-2-yl]-7H-purin-8-one;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0110uM
(2R,3R,4S,5R)-2-(6-amino-8-ethylpurin-9-yl)-5-[[4-aminooxybutyl(methyl)amino]methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0150uM
(2R,3R,4S,5R)-2-(6-amino-8-ethylpurin-9-yl)-5-[[4-aminooxybutyl(methyl)amino]methyl]oxolane-3,4-diol;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0150uM
(2R,3S,4R,5R)-2-[[4-aminooxybutyl(methyl)amino]methyl]-5-(6-aminopurin-9-yl)oxolane-3,4-diol;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0180uM
(2R,3S,4R,5R)-2-[[4-aminooxybutyl(methyl)amino]methyl]-5-(6-aminopurin-9-yl)oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0180uM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)purin-9-yl]-5-[[4-aminooxybutyl(methyl)amino]methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0490uM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)purin-9-yl]-5-[[4-aminooxybutyl(methyl)amino]methyl]oxolane-3,4-diol;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0490uM
(2R,3S,4R,5R)-2-[[2-aminooxyethyl(methyl)amino]methyl]-5-(6-aminopurin-9-yl)oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0550uM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)purin-9-yl]-5-[[2-aminooxyethyl(methyl)amino]methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.0860uM
(2R,3R,4S,5R)-2-[6-amino-8-(methylamino)purin-9-yl]-5-[[2-aminooxyethyl(methyl)amino]methyl]oxolane-3,4-diol;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic500.0860uM
3-[[(2R,3S,4R,5R)-5-(6-amino-8-methylpurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-methylamino]propanehydrazide1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.1700uM
3-[[(2R,3S,4R,5R)-5-(6-amino-8-methylpurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-methylamino]propanamide1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.4000uM
(2R,3R,4S,5R)-2-(6-amino-8-methylpurin-9-yl)-5-[(dimethylamino)methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic500.6000uM
3-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-methylamino]propanehydrazide1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic501.5000uM
[(2S,3S,4R,5R)-5-(6-amino-8-methylpurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-dimethylsulfanium1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic503.0000uM
[(2S,3S,4R,5R)-5-(6-amino-8-methylpurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-dimethylsulfanium chloride346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic503.0000uM
3-[[(2R,3S,4R,5R)-5-(6-amino-8-ethylpurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-methylamino]propanamide1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic504.0000uM
[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-dimethylsulfanium chloride346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic505.0000uM
3-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-methylamino]propanamide1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic507.0000uM
3-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl-methylamino]propanamide;sulfuric acid346361: Inhibition of human C-terminal His-tagged AdoMetDC assessed as release of 14CO2 from S-adenosyl-L-[carboxy-14C]methionineic507.0000uM
(2R,3R,4S,5R)-2-(6-aminopurin-9-yl)-5-[(dimethylamino)methyl]oxolane-3,4-diol1798891: AdoMetDC Inhibition Assay from Article 10.1021/jm801126a: “New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C(8) Substitution in Structural Analogues of S-Adenosylmethionine (dagger).”ic509.0000uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects methylation, decreases expression3
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression3
Cadmium Chloridedecreases expression, increases abundance, increases expression3
cobaltous chloridedecreases expression2
Resveratroldecreases activity, affects cotreatment, increases expression2
Acetaminophenincreases expression2
Estradiolincreases expression, increases reaction2
Hydrogen Peroxideaffects expression2
Nickelincreases expression2
Tobacco Smoke Pollutionincreases expression2
Tretinoindecreases expression2
Valproic Aciddecreases expression, increases expression2
Aflatoxin B1affects expression, decreases methylation, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
bismuth tripotassium dicitrateincreases expression1
triphenyl phosphateaffects expression1
alpha-pinenedecreases expression, increases abundance, affects cotreatment1
titanium dioxideincreases methylation1
beta-lapachoneincreases expression1
afimoxifenedecreases reaction, increases expression1
perfluorooctanoic aciddecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
3,3’,4,5’-tetrahydroxystilbenedecreases activity1
beta-methylcholineaffects expression1
bicalutamideincreases expression1
tamibarotenedecreases expression1

ChEMBL screening assays

39 unique, capped per target: 39 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1653935BindingRatio of Kinact to Kiapp for human AdoMetDC expressed in Escherichia coliNovel S-adenosylmethionine decarboxylase inhibitors for the treatment of human African trypanosomiasis. — Antimicrob Agents Chemother

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.