PDF

Summary

PDF (peptide deformylase, mitochondrial, HGNC:30012) is a protein-coding gene on chromosome 16q22.1, encoding Peptide deformylase, mitochondrial (Q9HBH1). Removes the formyl group from the N-terminal Met of newly synthesized proteins.

Protein synthesis proceeds after formylation of methionine by methionyl-tRNA formyl transferase (FMT) and transfer of the charged initiator f-met tRNA to the ribosome. In eubacteria and eukaryotic organelles the product of this gene, peptide deformylase (PDF), removes the formyl group from the initiating methionine of nascent peptides. In eubacteria, deformylation of nascent peptides is required for subsequent cleavage of initiating methionines by methionine aminopeptidase. The discovery that a natural inhibitor of PDF, actinonin, acts as an antimicrobial agent in some bacteria has spurred intensive research into the design of bacterial-specific PDF inhibitors. In human cells, only mitochondrial proteins have N-formylation of initiating methionines. Protein inhibitors of PDF or siRNAs of PDF block the growth of cancer cell lines but have no effect on normal cell growth. In humans, PDF function may therefore be restricted to rapidly growing cells.

Source: NCBI Gene 64146 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 9 total
• GTEx eGene: eQTL in 23 tissues, sQTL in 24 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.98 (unconstrained)
• MANE Select transcript: NM_022341

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30012
Approved symbol	PDF
Name	peptide deformylase, mitochondrial
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000258429
Ensembl biotype	protein_coding
OMIM	618720
Entrez	64146

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 nonsense_mediated_decay

MANE Select: ENST00000288022

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

ENST00000288022, ENST00001073636, ENST00001125246, ENST00001125247, ENST00001134389

RefSeq mRNA: 1 — MANE Select: NM_022341 NM_022341

CCDS: CCDS10875

Canonical transcript exons

ENST00000288022 — 2 exons

Exon	Start	End
ENSE00001031780	69329997	69330588
ENSE00001601028	69326913	69329179

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 81.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.3239 / max 45.6366, expressed in 1714 samples.

Highest expression (Bgee): male germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad, adult mammalian kidney, lobe of liver, stromal cell of endometrium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PDF is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 23 tissues and its splicing (sQTL) in 24 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 47 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	sqtl	7.1e-20	-0.55	16:69334093:C:A
Skin Sun Exposed Lower leg	eqtl	2.8e-19	-0.29	16:69334093:C:A
Artery Tibial	eqtl	1.0e-17	-0.35	16:69328549:C:G
Cells Cultured fibroblasts	eqtl	4.6e-17	-0.22	16:69338024:A:G
Skin Not Sun Exposed Suprapubic	eqtl	7.6e-17	-0.29	16:69322792:A:G
Skin Not Sun Exposed Suprapubic	sqtl	8.4e-17	-0.47	16:69207984:T:C
Artery Aorta	eqtl	2.7e-12	-0.38	16:69315882:T:C
Nerve Tibial	eqtl	3.5e-10	-0.25	16:69389213:A:G
Thyroid	eqtl	3.8e-10	-0.26	16:69207984:T:C
Brain Cortex	sqtl	6.6e-10	-0.65	16:69338024:A:G
Adipose Subcutaneous	sqtl	6.9e-10	-0.34	16:69321060:A:G
Artery Tibial	sqtl	8.7e-10	+0.41	16:69341755:G:A
Adipose Subcutaneous	eqtl	1.1e-09	-0.21	16:69334093:C:A
Brain Frontal Cortex BA9	sqtl	9.0e-09	-0.62	16:69338024:A:G
Esophagus Muscularis	eqtl	3.3e-08	-0.26	16:69341755:G:A
Lung	sqtl	3.9e-08	-0.36	16:69344542:A:G
Adipose Visceral Omentum	sqtl	8.8e-08	-0.32	16:69334093:C:A
Esophagus Mucosa	eqtl	1.7e-07	-0.19	16:69340558:G:C
Adipose Visceral Omentum	eqtl	6.2e-07	-0.21	16:69162112:T:C
Esophagus Muscularis	sqtl	9.8e-07	-0.39	16:69341755:G:A

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
157897	5.8335	1681
157896	0.8955	476
157895	0.5949	333

Top tissues by expression

showing 100 of 134 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.19	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.63	gold quality
adult mammalian kidney	UBERON:0000082	75.56	gold quality
right lobe of liver	UBERON:0001114	74.25	gold quality
stromal cell of endometrium	CL:0002255	74.00	gold quality
gastrocnemius	UBERON:0001388	73.19	gold quality
liver	UBERON:0002107	73.12	gold quality
mucosa of transverse colon	UBERON:0004991	72.99	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.69	gold quality
muscle of leg	UBERON:0001383	72.40	gold quality
kidney	UBERON:0002113	71.72	gold quality
metanephros cortex	UBERON:0010533	71.48	gold quality
cortex of kidney	UBERON:0001225	71.33	gold quality
skeletal muscle tissue	UBERON:0001134	71.07	gold quality
right adrenal gland	UBERON:0001233	70.18	gold quality
left adrenal gland	UBERON:0001234	70.01	gold quality
right adrenal gland cortex	UBERON:0035827	69.81	gold quality
monocyte	CL:0000576	69.80	gold quality
leukocyte	CL:0000738	69.76	gold quality
esophagus mucosa	UBERON:0002469	69.23	gold quality
left adrenal gland cortex	UBERON:0035825	69.15	gold quality
muscle tissue	UBERON:0002385	68.97	gold quality
superior frontal gyrus	UBERON:0002661	68.70	gold quality
body of pancreas	UBERON:0001150	68.48	gold quality
cortical plate	UBERON:0005343	68.20	gold quality
adrenal gland	UBERON:0002369	67.84	gold quality
primary visual cortex	UBERON:0002436	67.48	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	67.24	gold quality
endometrium	UBERON:0001295	66.88	gold quality
granulocyte	CL:0000094	66.63	gold quality
heart left ventricle	UBERON:0002084	66.34	gold quality
lower esophagus mucosa	UBERON:0035834	66.07	gold quality
esophagus	UBERON:0001043	65.82	gold quality
duodenum	UBERON:0002114	65.74	gold quality
saliva-secreting gland	UBERON:0001044	65.71	gold quality
minor salivary gland	UBERON:0001830	65.57	gold quality
transverse colon	UBERON:0001157	65.24	gold quality
body of stomach	UBERON:0001161	65.18	gold quality
bone marrow cell	CL:0002092	65.10	silver quality
skin of leg	UBERON:0001511	64.93	gold quality
left coronary artery	UBERON:0001626	64.75	gold quality
zone of skin	UBERON:0000014	64.68	gold quality
skin of abdomen	UBERON:0001416	64.57	gold quality
tonsil	UBERON:0002372	64.23	gold quality
heart	UBERON:0000948	64.08	gold quality
Brodmann (1909) area 9	UBERON:0013540	63.71	gold quality
thoracic aorta	UBERON:0001515	63.52	gold quality
fundus of stomach	UBERON:0001160	63.47	gold quality
colon	UBERON:0001155	63.42	gold quality
ascending aorta	UBERON:0001496	63.41	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	63.38	gold quality
ectocervix	UBERON:0012249	63.38	gold quality
left lobe of thyroid gland	UBERON:0001120	63.35	gold quality
placenta	UBERON:0001987	63.29	gold quality
stomach	UBERON:0000945	63.27	gold quality
myometrium	UBERON:0001296	63.22	gold quality
bone marrow	UBERON:0002371	63.16	gold quality
popliteal artery	UBERON:0002250	63.10	gold quality
tibial artery	UBERON:0007610	63.09	gold quality
apex of heart	UBERON:0002098	63.00	gold quality
right atrium auricular region	UBERON:0006631	62.90	gold quality
thyroid gland	UBERON:0002046	62.80	gold quality
body of uterus	UBERON:0009853	62.73	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	62.68	gold quality
intestine	UBERON:0000160	62.57	gold quality
small intestine	UBERON:0002108	62.56	gold quality
thoracic mammary gland	UBERON:0005200	62.53	gold quality
lower esophagus	UBERON:0013473	62.53	gold quality
right lobe of thyroid gland	UBERON:0001119	62.52	gold quality
lower esophagus muscularis layer	UBERON:0035833	62.51	gold quality
pancreas	UBERON:0001264	62.49	gold quality
adipose tissue	UBERON:0001013	62.48	gold quality
ventricular zone	UBERON:0003053	62.46	gold quality
left uterine tube	UBERON:0001303	62.45	gold quality
right coronary artery	UBERON:0001625	62.45	gold quality
omental fat pad	UBERON:0010414	62.44	gold quality
subcutaneous adipose tissue	UBERON:0002190	62.37	gold quality
anterior cingulate cortex	UBERON:0009835	62.27	gold quality
small intestine Peyer’s patch	UBERON:0003454	62.26	gold quality
right frontal lobe	UBERON:0002810	62.20	gold quality
prostate gland	UBERON:0002367	62.09	gold quality
multicellular organism	UBERON:0000468	61.99	gold quality
vagina	UBERON:0000996	61.91	gold quality
muscle layer of sigmoid colon	UBERON:0035805	61.84	gold quality
urinary bladder	UBERON:0001255	61.82	gold quality
upper lobe of left lung	UBERON:0008952	61.48	gold quality
spleen	UBERON:0002106	61.46	gold quality
descending thoracic aorta	UBERON:0002345	61.45	gold quality
lymph node	UBERON:0000029	61.38	gold quality
right ovary	UBERON:0002118	60.73	gold quality
uterine cervix	UBERON:0000002	60.71	gold quality
endocervix	UBERON:0000458	60.47	gold quality
rectum	UBERON:0001052	60.45	gold quality
Ammon’s horn	UBERON:0001954	60.43	gold quality
blood	UBERON:0000178	59.98	gold quality
putamen	UBERON:0001874	59.50	gold quality
adenohypophysis	UBERON:0002196	59.38	gold quality
left ovary	UBERON:0002119	59.33	gold quality
ovary	UBERON:0000992	59.18	gold quality
lung	UBERON:0002048	59.07	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.97

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Frontal cortex	tissue	20.7
Caudate putamen	tissue	18.2
Cerebellum	tissue	16.8	low
Basal ganglia	tissue	15.2	medium
Hippocampal formation	tissue	14.9
Cerebral cortex	tissue	14.5	medium
Putamen	tissue	14.5
Somatosensory cortex	tissue	14.5
Ventral forebrain	tissue	14.0
Occipital cortex	tissue	14.0
Temporal cortex	tissue	13.9
Olfactory bulb	tissue	13.7
Retrosplenial and cingulate cortex	tissue	13.6
Retrosplenial cortex	tissue	13.5
Insular cortex	tissue	13.4
Prefrontal cortex	tissue	13.2
Entorhinal cortex	tissue	13.1
Amygdala	tissue	13.0
Motor cortex	tissue	12.7
Septum	tissue	12.7
Corpus callosum	tissue	11.8
Periaqueductal gray	tissue	10.7
Hypothalamus	tissue	10.5
Midbrain	tissue	10.2
Spinal cord	tissue	10.0
Thalamus	tissue	9.9
Superior colliculi	tissue	9.9
Medulla oblongata	tissue	9.5
Pons	tissue	9.4
Substantia nigra	tissue	9.4
Hippocampus	tissue	9.4	medium
Choroid plexus	tissue	8.4
Postcentral gyrus	tissue	6.9
Locus coeruleus	tissue	6.5
Nucleus accumbens	tissue	6.1
Skeletal muscle	tissue	4.2	medium
Kidney	tissue	2.4	high
Stomach 1	tissue	2.3	medium
Salivary gland	tissue	2.2	medium
Pancreas	tissue	2.2	medium
Liver	tissue	2.1	medium
Duodenum	tissue	1.9	medium
Colon	tissue	1.7	medium
Adipose tissue	tissue	1.6	not detected
Parathyroid gland	tissue	1.5	medium
Vagina	tissue	1.4	medium
Small intestine	tissue	1.4	high
Thyroid gland	tissue	1.3	medium
Pituitary gland	tissue	1.2
Prostate	tissue	1.2	low
Bone marrow	tissue	1.2	not detected
Skin 1	tissue	1.1	high
Esophagus	tissue	1.1	medium
Spleen	tissue	1.1	low
Lymph node	tissue	1.0	medium
Adrenal gland	tissue	1.0	high
Appendix	tissue	0.9	medium
Breast	tissue	0.8	medium
Heart muscle	tissue	0.8	high
Rectum	tissue	0.8	medium

Brain sub-regions (HPA Brain Atlas): detected in 290; highest nTPM — Blood vessel (42.1), Dorsal hippocampus (14.9), Ventral hippocampus (13.8), Subiculum (12.6), White matter (11.8).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

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

28 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-520G-3P	98.91	67.38	1914
HSA-MIR-520H	98.91	67.38	1914
HSA-MIR-887-5P	98.82	65.90	1347
HSA-MIR-219A-2-3P	98.62	68.78	797
HSA-MIR-934	98.49	70.44	581
HSA-MIR-4691-5P	98.41	66.77	1343
HSA-MIR-6792-3P	98.41	66.86	1359
HSA-MIR-6810-5P	98.29	66.21	975
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-30C-1-3P	97.80	66.36	1499
HSA-MIR-30C-2-3P	97.80	66.45	1499
HSA-MIR-6788-5P	97.80	66.41	1532
HSA-MIR-3127-5P	97.52	65.24	786
HSA-MIR-509-3-5P	97.21	67.74	1517
HSA-MIR-509-5P	97.21	67.90	1512
HSA-MIR-4418	97.04	67.16	1372
HSA-MIR-212-5P	96.83	67.43	950
HSA-MIR-4652-5P	96.46	64.22	553
HSA-MIR-1258	96.08	67.74	700
HSA-MIR-187-3P	81.56	59.38	111

Functional genomics

gnomAD constraint: pLI 9.77e-17, LOEUF 1.98, missense Z -3.86 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000288022 — one region, missense o/e 1.23.

Literature-anchored findings (GeneRIF, showing 7)

• The inhibition of HsPDF may provide an explanation for the mechanism by which actinonin is cytotoxic against various human tumor cell lines. (PMID:14637138)
• Despite the lack of true S2’ and S3’ binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2’and P3’ positions of a formylated peptide substrate to turnover. (PMID:19236878)
• the origin, evolution and preservation of the COG8/PDF same-strand overlap follow similar mechanistic steps as those documented for antisense overlaps where gain and/or loss of splice sites and polyadenylation signals seems to drive the process. (PMID:21805148)
• these data reveals that PDF has several transcription start sites, the most important of which only 18 bp from the initiation codon. (PMID:22554513)
• This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers (PMID:23815882)
• c-myc regulated the expression of human PDF. (PMID:24675470)
• compound M7594_0037 exhibited potent anticancer activities against HeLa, A549 and MCF-7 cell lines with IC50s of 35.26, 29.63 and 24.63 muM, respectively. Molecular docking studies suggested that M7594_0037 and its three derivatives could interact with Human peptide deformylase by several conserved hydrogen bonds. (PMID:27023495)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdf	ENSDARG00000013950
mus_musculus	Pdf	ENSMUSG00000078931
rattus_norvegicus	Pdf	ENSRNOG00000022303
drosophila_melanogaster	CG31278	FBGN0051278
drosophila_melanogaster	CG31373	FBGN0051373

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
Streptomyces coelicolor A3(2)	Q9RD27	85.0%	Diamond
Bifidobacterium adolescentis ATCC 15703	A1A2Z1	83.5%	Diamond
Streptomyces avermitilis MA-4680 = NBRC 14893	Q825U9	83.5%	Diamond
Bifidobacterium longum NCC2705	Q8G534	83.5%	Diamond
Oryza sativa Japonica Group	B6RGY0	75.4%	Diamond
Solanum lycopersicum	Q9FUZ0	75.4%	Diamond
Arabidopsis thaliana	Q9FV53	74.2%	Diamond
Gloeobacter violaceus PCC 7421	Q7NJV3	47.4%	Diamond
Rickettsia conorii str. Malish 7	Q92JI7	43.0%	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
VPS4A	protein-coding	27183
NIP7	protein-coding	51388
SNTB2	protein-coding	6645
COG8	protein-coding	84342
UTP4	protein-coding	84916
DERPC	protein-coding	113455421
HAS3	protein-coding	3038
CHTF8	protein-coding	54921
TMED6	protein-coding	146456
TERF2	protein-coding	7014
CYB5B	protein-coding	80777

Protein

Protein identifiers

Peptide deformylase, mitochondrial — Q9HBH1 (reviewed: Q9HBH1)

Alternative names: Polypeptide deformylase

All UniProt accessions (1): Q9HBH1

UniProt curated annotations — full annotation on UniProt →

Function. Removes the formyl group from the N-terminal Met of newly synthesized proteins.

Subunit / interactions. Homodimer.

Subcellular location. Mitochondrion.

Tissue specificity. Ubiquitous.

Cofactor. Binds 1 Co(2+) ion.

Similarity. Belongs to the polypeptide deformylase family.

RefSeq proteins (1): NP_071736* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023635	Peptide_deformylase	Family
IPR036821	Peptide_deformylase_sf	Homologous_superfamily

Pfam: PF01327

Enzyme classification (BRENDA)

• EC 3.5.1.88 — peptide deformylase (BRENDA: 55 organisms, 191 substrates, 745 inhibitors, 156 Km, 135 kcat entries)

Substrate kinetics (BRENDA)

95 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
N-FORMYL-MET-ALA-SER	0.25–48	17
FORMYL-MET-ALA	0.14–28	15
FORMYL-MET-ALA-SER	0.2–70	15
FORMYL-MET-ALA-LYS-TYR	0.34–7.6	7
N-FORMYL-MET-ALA	2.9–480	7
N-FORMYLMETHIONYL-LEU-P-NITROANILIDE	0.018–0.028	4
N-FORMYL-L-MET-L-VAL	7.1–12.4	3
N-FORMYL-MET-SER-ASN-GLU	2–5.5	3
N-FORMYL-NLE-ALA-SER	0.6–11	3
FORMYL-MET-LEU-P-NITROANILIDE	0.024–0.047	2
FORMYL-MTHQ	1.56–2.287	2
N-FORMYL-ASP(NH2)	0.74–1	2
N-FORMYL-BETA-THIAPHENYLALANYL-LYS-P-NITROANILID	0.027–0.03	2
N-FORMYL-GLY(NH2)	2.9–4.3	2
N-FORMYL-MET-LEU-GLU	8–12	2

Catalyzed reactions (Rhea)

• N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl-[peptide] + formate (RHEA:24420)

UniProt features (26 total): helix 10, binding site 6, strand 5, transit peptide 1, chain 1, sequence variant 1, region of interest 1, active site 1

Structure

Experimental structures (PDB)

2 structures by resolution:

PDB	Title	Method	Resolution (Å)
3G5K	Structure and activity of human mitochondrial peptide deformylase, a novel cancer target	X-RAY DIFFRACTION	1.7
3G5P	Structure and activity of human mitochondrial peptide deformylase, a novel cancer target	X-RAY DIFFRACTION	1.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HBH1-F1	86.21	0.75

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Hydrolases, Metabolic proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): mitochondria; nucleoplasm

Antibody reliability (HPA): IH approved · IF approved

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 (1)

Position	Role
215

Ligand- & substrate-binding residues (6)

Position	Role
71	substrate
169	substrate
171	substrate
172	Co(2+)
214	Co(2+)
218	Co(2+)

Function

Pathways and Gene Ontology

Reactome pathways

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

MSigDB gene sets: 85 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, chr16q22, GOBP_TRANSLATION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP, KIM_WT1_TARGETS_DN, LIU_COMMON_CANCER_GENES, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS_IN_LINEAR_AMIDES, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS, GRABARCZYK_BCL11B_TARGETS_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, GOBP_POSITIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION

GO Biological Process (4): translation (GO:0006412), positive regulation of cell population proliferation (GO:0008284), peptidyl-methionine modification (GO:0018206), post-translational protein modification (GO:0043687)

GO Molecular Function (3): peptide deformylase activity (GO:0042586), metal ion binding (GO:0046872), hydrolase activity (GO:0016787)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

16 GO namespaces:

Category	Terms
protein modification process	2
peptidyltransferase activity	1
translational initiation	1
translational elongation	1
translational termination	1
macromolecule biosynthetic process	1
protein metabolic process	1
protein biosynthetic process	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	1
cation binding	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 8 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO term	NS	Evidence
peptidyl-methionine modification	BP	direct assay
positive regulation of cell population proliferation	BP	mutant phenotype
post-translational protein modification	BP	direct assay
mitochondrion	CC	direct assay
peptide deformylase activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 1,118 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDF	MTFMT	Q96DP5	773
PDF	METAP1D	Q6UB28	605
PDF	MRRF	Q96E11	547
PDF	METAP1	P53582	546
PDF	TSFM	P43897	460
PDF	MARS2	Q96GW9	376
PDF	MARS1	P56192	367
PDF	METAP2	P50579	350
PDF	HIBCH	Q6NVY1	334
PDF	HSPE1	P61604	332
PDF	MTRFR	Q9H3J6	328
PDF	PCCB	P05166	324
PDF	DERA	Q9Y315	322
PDF	DHODH	Q02127	314
PDF	XPNPEP3	Q9NQH7	313

IntAct

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

3 partners by confidence:

Partner	Interaction type	MIscore	Records
PRSS48	physical association	0.400	1
MYO5B	physical association	0.000	1
RAC1	physical association	0.000	1

BioGRID (104 interactions; top human partners by supporting records): PTCH1 (Affinity Capture-MS; 3 records), TMEM25 (Affinity Capture-MS; 3 records), A2M (Affinity Capture-MS; 2 records), ATP5A1 (Cross-Linking-MS (XL-MS); 2 records), CETN1 (Affinity Capture-MS; 2 records), CRP (Affinity Capture-MS; 2 records), DEFA5 (Affinity Capture-MS; 2 records), ERBB3 (Affinity Capture-MS; 2 records), KIF1B (Affinity Capture-MS; 2 records), MRPS34 (Affinity Capture-MS; 2 records), OLFM4 (Affinity Capture-MS; 2 records), P4HA3 (Affinity Capture-MS; 2 records), PROC (Affinity Capture-MS; 2 records), ACTR5 (Affinity Capture-MS), ADAM21 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for PDF: 9 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	0
Benign	2

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 23 predictions of 176):

Position(s)	Effect	Δscore	Sites
16:69329180–69329182	acceptor_loss	0.9400	7
16:69329817	donor_gain	0.9400
16:69329888	donor_gain	0.9000
16:69329798	donor_gain	0.8200
16:69329995–69329996	donor_loss	0.8000	6
16:69329997	donor_loss	0.7900	3
16:69329269	donor_gain	0.7800
16:69329672	donor_gain	0.7600
16:69329336	donor_gain	0.7400
16:69329998	donor_loss	0.7300

AlphaMissense

517 missense substitutions predicted likely pathogenic (of 1,541 scored), across 124 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
M228	9	0.881	0.965
H214	8	0.985	0.989
H218	8	0.978	0.993
D217	8	0.975	0.991
D226	8	0.952	0.991
S174	8	0.901	0.995
N155	8	0.899	0.992
F233	8	0.828	0.986
F153	8	0.798	0.988
E215	7	0.975	0.996
C172	7	0.964	0.988
E170	7	0.960	0.991
F178	7	0.959	0.990
F224	7	0.959	0.985
W207	7	0.953	0.988
M103	7	0.930	0.977
S112	7	0.910	0.991
Q213	7	0.905	0.992
W238	7	0.898	0.976
F64	7	0.890	0.955

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

2 prognostic cancer types:

Cancer	Prognostic	p-value
Glioblastoma Multiforme (validation)	unfavorable	0.000235
Rectum Adenocarcinoma (validation)	favorable	0.000414

Disease associations

OMIM: gene MIM:618720 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST005951_23	Body mass index	5e-11
GCST007006_16	Logical memory (delayed recall) in normal cognition	7e-7

EFO canonical traits (from GWAS)

2 canonical traits:

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4647 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

63 measured of 76 human assays (95 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
(R)-2-Butyl-N*1*-((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-N*4*-hydroxy-succinamide	IC50	1 nM
CHEMBL4637933	IC50	2.8 nM
CHEMBL4638057	IC50	3 nM
CHEMBL4632607	IC50	3.6 nM
CHEMBL4643984	IC50	4.2 nM
CHEMBL4639327	IC50	4.9 nM
CHEMBL4649534	IC50	4.9 nM
CHEMBL4641416	IC50	5 nM
CHEMBL4636545	IC50	5 nM
CHEMBL4643967	IC50	5.5 nM
CHEMBL4636221	IC50	5.9 nM
CHEMBL4634572	IC50	5.9 nM
(S)-2-[(R)-2-Cyclohexylmethyl-3-(formyl-hydroxy-amino)-propionylamino]-3,3,N,N-tetramethyl-butyramide	IC50	6 nM
CHEMBL4637166	IC50	6.1 nM
CHEMBL4640974	IC50	6.4 nM
CHEMBL4645966	IC50	6.5 nM
CHEMBL4635093	IC50	7 nM
CHEMBL4637631	IC50	7.1 nM
CHEMBL4642360	IC50	7.2 nM
CHEMBL4635263	IC50	7.2 nM
(S)-2-[(R)-2-Cyclopentylmethyl-3-(formyl-hydroxy-amino)-propionylamino]-3,3,N,N-tetramethyl-butyramide	IC50	8 nM
CHEMBL4645936	IC50	8.7 nM
CHEMBL4646467	IC50	8.8 nM
CHEMBL4641901	IC50	8.9 nM
CHEMBL4640884	IC50	9.3 nM
CHEMBL4644600	IC50	9.4 nM
CHEMBL4638180	IC50	9.5 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-4-methyl-pentanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	10 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-heptanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	10 nM
CHEMBL4636076	IC50	11 nM
CHEMBL4645201	IC50	13 nM
CHEMBL4643686	IC50	16 nM
(S)-2-Mercaptomethyl-hexanoic acid [(S)-5-amino-1-(4-nitro-phenylcarbamoyl)-pentyl]-amide	KI	19 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-hex-5-enoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	20 nM
(S)-2-[(R)-2-Ethylsulfanylmethyl-3-(formyl-hydroxy-amino)-propionylamino]-3,3,N,N-tetramethyl-butyramide	IC50	20 nM
(S)-2-[(R)-2-Benzyl-3-(formyl-hydroxy-amino)-propionylamino]-3,3,N,N-tetramethyl-butyramide	IC50	20 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-5-methyl-hexanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	20 nM
(S)-2-[(R)-2-Cyclopentyl-3-(formyl-hydroxy-amino)-propionylamino]-3,3,N,N-tetramethyl-butyramide	IC50	20 nM
CHEMBL4649755	IC50	29 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-pent-4-enoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	30 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-octanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	30 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-hex-4-ynoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	30 nM
CHEMBL4641571	IC50	30 nM
CHEMBL5191348	IC50	30 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-nonanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	40 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-decanoic acid [1-((S)-dimethyl-carbamoyl)-2,2-dimethyl-propyl]-amide	IC50	50 nM
(R)-2-[(Formyl-hydroxy-amino)-methyl]-pentanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	50 nM
(R)-N-((S)-1-Dimethylcarbamoyl-2,2-dimethyl-propyl)-2-[(formyl-hydroxy-amino)-methyl]-3-methyl-butyramide	IC50	50 nM
(S)-2-{(R)-2-[(Formyl-hydroxy-amino)-methyl]-butyrylamino}-3,3,N,N-tetramethyl-butyramide	IC50	70 nM
(S)-2-[(Formyl-hydroxy-amino)-methyl]-hexanoic acid ((S)-1-dimethylcarbamoyl-2,2-dimethyl-propyl)-amide	IC50	70 nM

ChEMBL bioactivities

77 potent at pChembl≥5 of 87 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
9.52	Ki	0.3	nM	ACTINONIN
9.00	IC50	1	nM	CHEMBL122067
8.82	IC50	1.5	nM	ACTINONIN
8.56	IC50	2.78	nM	CHEMBL4637933
8.52	IC50	2.99	nM	CHEMBL4638057
8.45	IC50	3.58	nM	CHEMBL4632607
8.42	IC50	3.77	nM	CHEMBL4641062
8.39	IC50	4.11	nM	CHEMBL4635911
8.37	IC50	4.24	nM	CHEMBL4643984
8.31	IC50	4.92	nM	CHEMBL4639327
8.31	IC50	4.85	nM	CHEMBL4649534
8.30	IC50	5.01	nM	CHEMBL4641416
8.30	IC50	5.01	nM	CHEMBL4636545
8.26	IC50	5.48	nM	CHEMBL4643967
8.23	IC50	5.87	nM	CHEMBL4636221
8.23	IC50	5.87	nM	CHEMBL4634572
8.22	IC50	6	nM	CHEMBL90193
8.21	IC50	6.12	nM	CHEMBL4637166
8.19	IC50	6.42	nM	CHEMBL4640974
8.19	IC50	6.47	nM	CHEMBL4645966
8.15	IC50	7.15	nM	CHEMBL4642360
8.15	IC50	7.01	nM	CHEMBL4635093
8.15	IC50	7.08	nM	CHEMBL4637631
8.15	IC50	7	nM	CHEMBL431210
8.14	IC50	7.19	nM	CHEMBL4635263
8.10	IC50	8	nM	CHEMBL316099
8.06	IC50	8.74	nM	CHEMBL4645936
8.05	IC50	8.94	nM	CHEMBL4641901
8.05	IC50	8.81	nM	CHEMBL4646467
8.03	IC50	9.42	nM	CHEMBL4644600
8.03	IC50	9.26	nM	CHEMBL4640884
8.02	IC50	9.53	nM	CHEMBL4638180
8.00	IC50	10	nM	CHEMBL96864
8.00	IC50	10	nM	CHEMBL413726
8.00	IC50	10	nM	ACTINONIN
7.96	IC50	10.9	nM	CHEMBL4636076
7.88	IC50	13.1	nM	CHEMBL4645201
7.79	IC50	16.1	nM	CHEMBL4643686
7.72	Ki	19	nM	CHEMBL325246
7.70	IC50	20	nM	CHEMBL540441
7.70	IC50	20	nM	CHEMBL328502
7.70	IC50	20	nM	CHEMBL91882
7.70	IC50	20	nM	CHEMBL91835
7.70	IC50	20	nM	CHEMBL328688
7.53	IC50	29.3	nM	CHEMBL4649755
7.52	IC50	30	nM	ACTINONIN
7.52	IC50	30.2	nM	CHEMBL4641571
7.52	IC50	30	nM	CHEMBL5191348
7.52	IC50	30	nM	CHEMBL91461
7.52	IC50	30	nM	CHEMBL93648

PubChem BioAssay actives

77 with measured affinity, of 300 total; 50 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)-N’-hydroxy-N-[(2S)-1-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]-2-pentylbutanediamide	157064: Binding affinity towards Peptide deformylase	ki	0.0003	uM
(2R)-2-butyl-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-N’-hydroxybutanediamide	156923: Compound was evaluated for inhibition of peptide deformylase, PDF.Ni of Escherichia coli	ic50	0.0010	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(5-methyl-1,3-thiazol-2-yl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0028	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(4-methyl-1,3-thiazol-2-yl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0030	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(4-methylphenyl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0036	uM
(3R)-3-(cyclopentylmethyl)-N-hydroxy-4-oxo-4-[(6S)-6-(3-phenyl-1,2,4-oxadiazol-5-yl)-5-azaspiro[2.4]heptan-5-yl]butanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0038	uM
(3R)-3-(cyclopentylmethyl)-4-[(6S)-6-[3-[4-fluoro-2-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0041	uM
(3R)-4-[(6S)-6-[3-(4-butylphenyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-3-(cyclopentylmethyl)-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0042	uM
(6S)-N-(5-fluoro-2-pyridinyl)-5-[(2R)-2-[2-(hydroxyamino)-2-oxoethyl]hexanoyl]-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0049	uM
(3R)-3-(cyclopentylmethyl)-4-[(6S)-6-[3-[2-fluoro-4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0049	uM
(3R)-3-(cyclopentylmethyl)-4-[(6S)-6-[3-(4-cyclopropylphenyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0050	uM
(3R)-3-(cyclopentylmethyl)-4-[(6S)-6-[3-(5-fluoro-2-pyridinyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0050	uM
(3R)-4-[(6S)-6-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-3-(cyclopentylmethyl)-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0055	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-pyrazin-2-yl-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0059	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(5-fluoro-2-pyridinyl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0059	uM
(2S)-2-[[(2R)-2-(cyclohexylmethyl)-3-[formyl(hydroxy)amino]propanoyl]amino]-N,N,3,3-tetramethylbutanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0060	uM
(6S)-N-(4-bromophenyl)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0061	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-phenyl-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0064	uM
(3R)-4-[(6S)-6-[3-[2-chloro-4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-3-(cyclopentylmethyl)-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0065	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-[4-fluoro-2-(trifluoromethyl)phenyl]-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0070	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hexanamide	156922: Antibacterial activity against Escherichia coli Peptide deformylase. Ni	ic50	0.0070	uM
(3R)-3-(cyclopentylmethyl)-N-hydroxy-4-oxo-4-[(6S)-6-[3-(2,3,5-trifluorophenyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]butanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0071	uM
(3R)-3-(cyclopentylmethyl)-N-hydroxy-4-oxo-4-[(6S)-6-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]butanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0072	uM
(2S)-1-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(5-fluoro-2-pyridinyl)-4-methylidenepyrrolidine-2-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0072	uM
(2S)-2-[[(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl]amino]-N,N,3,3-tetramethylbutanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0080	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(1,3-thiazol-2-yl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0087	uM
(3R)-3-(cyclopentylmethyl)-4-[(6S)-6-[3-(4-ethylphenyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-N-hydroxy-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0088	uM
(2S)-1-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(5-methyl-1,3-thiazol-2-yl)pyrrolidine-2-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0089	uM
(3R)-3-(cyclopentylmethyl)-N-hydroxy-4-[(6S)-6-[3-(4-methylphenyl)-1,2,4-oxadiazol-5-yl]-5-azaspiro[2.4]heptan-5-yl]-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0093	uM
(6S)-5-[(2R)-2-[2-(hydroxyamino)-2-oxoethyl]hexanoyl]-N-(5-methyl-1,3-thiazol-2-yl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0094	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-pyrimidin-4-yl-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0095	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]heptanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0100	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]-4-methylpentanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0100	uM
(2S)-1-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(5-fluoro-2-pyridinyl)pyrrolidine-2-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0109	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-pyridazin-3-yl-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0131	uM
(3R)-3-(cyclopentylmethyl)-N-hydroxy-4-oxo-4-[(6S)-6-(3-pyrazin-2-yl-1,2,4-oxadiazol-5-yl)-5-azaspiro[2.4]heptan-5-yl]butanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0161	uM
(2S)-N-[(2S)-6-amino-1-(4-nitroanilino)-1-oxohexan-2-yl]-2-(sulfanylmethyl)hexanamide	156928: Compound was evaluated for inhibition of peptide deformylase, PDF.Fe of Escherichia coli	ki	0.0190	uM
(2S)-2-[[(2R)-2-benzyl-3-[formyl(hydroxy)amino]propanoyl]amino]-N,N,3,3-tetramethylbutanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0200	uM
(2S)-2-[[(2R)-2-cyclopentyl-3-[formyl(hydroxy)amino]propanoyl]amino]-N,N,3,3-tetramethylbutanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0200	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]-5-methylhexanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0200	uM
(2S)-2-[[(2R)-2-(ethylsulfanylmethyl)-3-[formyl(hydroxy)amino]propanoyl]amino]-N,N,3,3-tetramethylbutanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0200	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hex-5-enamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0200	uM
(3R)-3-(cyclopentylmethyl)-N-hydroxy-4-[(6S)-6-(3-methyl-1,2,4-oxadiazol-5-yl)-5-azaspiro[2.4]heptan-5-yl]-4-oxobutanamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0293	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]hex-4-ynamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0300	uM
(2S)-2-[[(2R)-2-[[formyl(hydroxy)amino]methyl]pent-4-enoyl]amino]-N,N,3,3-tetramethylbutanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0300	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]octanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0300	uM
(2R)-N’-hydroxy-N-[(2S)-1-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]-2-pentylbutanediamide	1869130: Inhibition of human PDF by spectrophotometric analysis	ic50	0.0300	uM
(6S)-5-[(2R)-2-(cyclopentylmethyl)-4-(hydroxyamino)-4-oxobutanoyl]-N-(1-methylpyrazol-4-yl)-5-azaspiro[2.4]heptane-6-carboxamide	1658869: Inhibition of human PDF expressed in Escherichia coli BL21 pLysS using formyl-Met-Ala-His-Ala peptide as substrate measured after 1 hr by fluorescamine-based fluorescence assay	ic50	0.0302	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]nonanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0400	uM
(2R)-N-[(2S)-1-(dimethylamino)-3,3-dimethyl-1-oxobutan-2-yl]-2-[[formyl(hydroxy)amino]methyl]decanamide	156924: Inhibition against Escherichia coli peptide deformylase	ic50	0.0500	uM

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
lead acetate	decreases expression	1
arsenite	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
Oxaliplatin	increases expression, decreases response to substance	1
Sunitinib	increases expression	1
Amiodarone	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Fluorouracil	increases expression, decreases response to substance	1
Oxygen	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1

ChEMBL screening assays

22 unique, capped per target: 22 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1811207	Binding	Inhibition of human peptide deformylase at 10 uM after 1 hr by fluorescence polarization based competition assay	Identification of benzofuran-4,5-diones as novel and selective non-hydroxamic acid, non-peptidomimetic based inhibitors of human peptide deformylase. — *Bioorg Med Chem Lett*

Clinical trials (associated diseases)

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

Predicted chemistry — Sugi Predict

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