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
• Druggable target: yes
• 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: 1 — 1 protein_coding

ENST00000288022

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.

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

134 total, 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

Single-cell (SCXA)

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

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

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

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

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

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

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), 1 shown:

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

UniProt features (25 total): helix 9, 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.

PDB	Method	Resolution (Å)
3G5K	X-RAY DIFFRACTION	1.7
3G5P	X-RAY DIFFRACTION	1.7

Predicted structure (AlphaFold)

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

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): 215

Ligand- & substrate-binding residues (6): 71; 169; 171; 172; 214; 218

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

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 (5): translation (GO:0006412), positive regulation of cell population proliferation (GO:0008284), peptidyl-methionine modification (GO:0018206), post-translational protein modification (GO:0043687), obsolete co-translational protein modification (GO:0043686)

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

Rollup of top GO terms by namespace:

Category	Terms
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
peptidyl-amino acid modification	1
protein modification 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

Protein interactions and networks

STRING

1628 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDF	MTFMT	Q96DP5	806
PDF	METAP1D	Q6UB28	659
PDF	METAP1	P53582	595
PDF	TSFM	P43897	572
PDF	MRRF	Q96E11	543
PDF	RPL31	P12947	461
PDF	MTRFR	Q9H3J6	439
PDF	SHMT2	P34897	434
PDF	CLPP	Q16740	432
PDF	METAP2	P50579	432
PDF	MTIF2	P46199	425
PDF	MARS1	P56192	420
PDF	MRPL58	Q14197	416
PDF	TUFM	P49411	406
PDF	GUF1	Q8N442	404

IntAct

102 interactions, top by confidence:

A	B	Type	Score
STAT2	STAT1	psi-mi:“MI:0914”(association)	0.930
KIF1B	YWHAZ	psi-mi:“MI:0914”(association)	0.740
CETN1	SFI1	psi-mi:“MI:0914”(association)	0.640
P4HA3	FAM171A2	psi-mi:“MI:0914”(association)	0.640
BPNT1	GTPBP10	psi-mi:“MI:0914”(association)	0.530
NPPA	A2ML1	psi-mi:“MI:0914”(association)	0.530
DEFA5	NUDT19	psi-mi:“MI:0914”(association)	0.530
ERBB3	SLC31A1	psi-mi:“MI:0914”(association)	0.530
ADAM33	LRP5	psi-mi:“MI:0914”(association)	0.530
NRROS	NDUFA3	psi-mi:“MI:0914”(association)	0.530
ENPP7	TUBB3	psi-mi:“MI:0914”(association)	0.530
CRP	QSOX1	psi-mi:“MI:0914”(association)	0.530
MRPS34	ZZEF1	psi-mi:“MI:0914”(association)	0.530
UQCRFS1	NDUFAB1	psi-mi:“MI:0914”(association)	0.530
SSMEM1	ENDOD1	psi-mi:“MI:0914”(association)	0.530
MCOLN2	MCOLN3	psi-mi:“MI:0914”(association)	0.530
RNF7	SOCS7	psi-mi:“MI:0914”(association)	0.530
PRSS48	PDF	psi-mi:“MI:0915”(physical association)	0.400
TACC3	DHRS2	psi-mi:“MI:0914”(association)	0.350
Mad2l1	MAD1L1	psi-mi:“MI:0914”(association)	0.350
Shoc2	GABPB1	psi-mi:“MI:0914”(association)	0.350
PARD6B	PARD3	psi-mi:“MI:0914”(association)	0.350
Smc3	PDS5B	psi-mi:“MI:0914”(association)	0.350
Nek2	WDR46	psi-mi:“MI:0914”(association)	0.350
Oxnad1	KPNA6	psi-mi:“MI:0914”(association)	0.350
Tnpo1	CCHCR1	psi-mi:“MI:0914”(association)	0.350
Cdc6		psi-mi:“MI:0914”(association)	0.350

BioGRID (103): PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS), PDF (Affinity Capture-MS)

ESM2 similar proteins: O35465, O60294, P50336, P82923, Q14318, Q16512, Q2KJF7, Q2TBI8, Q32NY4, Q3B7U9, Q501J2, Q58CR3, Q5E9V4, Q5T440, Q5VT66, Q5ZIW1, Q60HD5, Q6AYG0, Q6IN84, Q6P9U1, Q864R5, Q8BNV1, Q8BZG5, Q8CAK1, Q8IZ69, Q8N9H8, Q8NE01, Q8TD43, Q8VD52, Q91WM2, Q920N2, Q969S8, Q96EN8, Q96EY9, Q96FB5, Q99J25, Q9BQD7, Q9BRQ3, Q9BXW7, Q9CW42

Diamond homologs: A0LEJ7, A0M3P3, A1A2Z1, A1UUB4, A2BNK7, A4VFH8, A4XNB3, A5ILS1, A5VDM3, A5WBG1, A6H0E7, A6L7J9, A6L9R8, A9ILK4, B0SHH1, B0SQM2, B1LB14, B1XJP0, B1ZMD5, B2RMJ1, B3EE19, B3ETT4, B3PGY7, B3QCH1, B3QPU5, B4SKH7, B6RGY0, B8CWS6, B9K7G9, C0QI55, C1DFV8, O66847, P43522, P63913, P63914, P96113, Q04RW4, Q051Q7, Q07TX0, Q0VTE1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

444 predictions. Top by Δscore:

Variant	Effect	Δscore
16:69329853:T:TA	donor_gain	0.9900
16:69329178:CC:C	acceptor_gain	0.9800
16:69329179:CC:C	acceptor_gain	0.9800
16:69329175:CAGCC:C	acceptor_gain	0.9700
16:69329177:GCCC:G	acceptor_loss	0.9700
16:69329179:CCTGC:C	acceptor_loss	0.9700
16:69329180:C:CA	acceptor_loss	0.9700
16:69329181:T:G	acceptor_loss	0.9700
16:69329177:GCC:G	acceptor_gain	0.9600
16:69329178:CCC:C	acceptor_gain	0.9600
16:69329180:C:CC	acceptor_gain	0.9600
16:69329182:G:C	acceptor_loss	0.9600
16:69329269:C:A	donor_gain	0.9600
16:69329817:T:C	donor_gain	0.9600
16:69329884:T:TA	donor_gain	0.9600
16:69329888:T:TA	donor_gain	0.9600
16:69330171:C:CA	donor_gain	0.9600
16:69329924:T:TA	donor_gain	0.9500
16:69330011:G:GA	donor_gain	0.9500
16:69329268:T:TA	donor_gain	0.9400
16:69329991:CCGCA:C	donor_loss	0.9400
16:69329992:CGCAC:C	donor_loss	0.9400
16:69329993:GCAC:G	donor_loss	0.9400
16:69329994:CA:C	donor_loss	0.9400
16:69329995:ACCTG:A	donor_loss	0.9400
16:69329996:CCT:C	donor_loss	0.9400
16:69329336:C:A	donor_gain	0.9300
16:69329997:C:G	donor_loss	0.9300
16:69329176:AGCC:A	acceptor_gain	0.9200
16:69329258:T:TA	donor_gain	0.9200

AlphaMissense

1541 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:69329110:T:A	E215V	0.996
16:69330049:G:C	S174R	0.995
16:69330049:G:T	S174R	0.995
16:69330051:T:G	S174R	0.995
16:69329109:C:A	E215D	0.994
16:69329109:C:G	E215D	0.994
16:69329100:G:C	H218Q	0.993
16:69329100:G:T	H218Q	0.993
16:69329119:A:T	I212N	0.993
16:69329115:C:A	Q213H	0.992
16:69329115:C:G	Q213H	0.992
16:69330106:G:C	N155K	0.992
16:69330106:G:T	N155K	0.992
16:69329077:T:A	D226V	0.991
16:69329104:T:A	D217V	0.991
16:69329128:G:T	A209D	0.991
16:69329179:C:T	G192E	0.991
16:69330061:C:A	E170D	0.991
16:69330061:C:G	E170D	0.991
16:69330235:G:C	S112R	0.991
16:69330235:G:T	S112R	0.991
16:69330237:T:G	S112R	0.991
16:69329102:G:C	H218D	0.990
16:69330038:A:G	F178S	0.990
16:69330047:A:T	V175D	0.990
16:69329105:C:G	D217H	0.989
16:69329112:G:C	H214Q	0.989
16:69329112:G:T	H214Q	0.989
16:69329114:G:C	H214D	0.989
16:69329114:G:T	H214N	0.989

dbSNP variants (sampled 300 via entrez): RS1000159915 (16:69326488 T>G), RS1000204668 (16:69329766 G>A,C), RS1000354335 (16:69328587 A>G), RS1000422460 (16:69329415 G>A,C), RS1000883985 (16:69331329 G>A), RS1000990978 (16:69332311 C>T), RS1001670729 (16:69329239 T>A), RS1002377120 (16:69331865 T>C), RS1002450664 (16:69332108 C>T), RS1002549071 (16:69328157 A>G), RS1002601362 (16:69328343 A>AT), RS1002918508 (16:69330106 G>A,T), RS1003190784 (16:69331792 C>T), RS1003209922 (16:69331490 G>A,T), RS1003344646 (16:69329619 G>A)

Disease associations

OMIM: gene MIM:618720 | disease phenotypes: MIM:611182

GenCC curated gene-disease

Mondo (1): COG8-congenital disorder of glycosylation (MONDO:0012635)

Orphanet (1): COG8-CDG (Orphanet:95428)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005951_13	Body mass index	5.000000e-11
GCST007006_16	Logical memory (delayed recall) in normal cognition	7.000000e-07

EFO canonical traits (2, from GWAS)

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

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566987	Congenital Disorder Of Glycosylation, Type IIH (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4647 (SINGLE PROTEIN)

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

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	decreases response to substance, increases expression	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)

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