Structure of PDB 3g5k Chain C Binding Site BS01

Receptor Information
>3g5k Chain C (length=183) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMSFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVG
LSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRV
LDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAAR
IIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND
Ligand information
Ligand IDBB2
InChIInChI=1S/C19H35N3O5/c1-4-5-6-8-14(11-16(24)21-27)18(25)20-17(13(2)3)19(26)22-10-7-9-15(22)12-23/h13-15,17,23,27H,4-12H2,1-3H3,(H,20,25)(H,21,24)/t14-,15+,17+/m1/s1
InChIKeyXJLATMLVMSFZBN-VYDXJSESSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCC[CH](CC(=O)NO)C(=O)N[CH](C(C)C)C(=O)N1CCC[CH]1CO
OpenEye OEToolkits 1.5.0CCCCCC(CC(=O)NO)C(=O)NC(C(C)C)C(=O)N1CCCC1CO
ACDLabs 10.04O=C(N1C(CO)CCC1)C(NC(=O)C(CC(=O)NO)CCCCC)C(C)C
CACTVS 3.341
OpenEye OEToolkits 1.5.0		CCCCC[C@H](CC(=O)NO)C(=O)N[C@@H](C(C)C)C(=O)N1CCC[C@H]1CO
FormulaC19 H35 N3 O5
NameACTINONIN;
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
ChEMBLCHEMBL308333
DrugBankDB04310
ZINCZINC000003979014
PDB chain3g5k Chain C Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3g5k Structure and activity of human mitochondrial peptide deformylase, a novel cancer target
Resolution1.7 Å
Binding residue
(original residue number in PDB)		C50 V51 G52 Q57 R85 P111 E112 G113 C114 E115 W149 R152 H156 E157 H160
Binding residue
(residue number reindexed from 1)		C48 V49 G50 Q55 R83 P109 E110 G111 C112 E113 W147 R150 H154 E155 H158
Annotation score1
Binding affinityBindingDB: IC50=1.5nM,Ki=0.300000nM
Enzymatic activity
Catalytic site (original residue number in PDB) G52 Q57 C114 E115 H156 E157 H160
Catalytic site (residue number reindexed from 1) G50 Q55 C112 E113 H154 E155 H158
Enzyme Commision number 3.5.1.88: peptide deformylase.
Gene Ontology
Molecular Function
GO:0042586 peptide deformylase activity

View graph for
Molecular Function
External links
PDB RCSB:3g5k, PDBe:3g5k, PDBj:3g5k
PDBsum3g5k
PubMed19236878
UniProtQ9HBH1|DEFM_HUMAN Peptide deformylase, mitochondrial (Gene Name=PDF)

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