Structure of PDB 3pn4 Chain A Binding Site BS01

Receptor Information
>3pn4 Chain A (length=181) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVG
LNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAE
VVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQ
VLDSIREELEALEKKYEEKTGLPSPERVEAR
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 chain3pn4 Chain A Residue 501 [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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PDB3pn4 Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G41 I42 G43 Q48 D88 G90 C91 L92 Y98 R129 H133 E134 H137
Binding residue
(residue number reindexed from 1)		G41 I42 G43 Q48 D88 G90 C91 L92 Y98 R129 H133 E134 H137
Annotation score1
Binding affinityMOAD: Ki=140nM
PDBbind-CN: -logKd/Ki=6.85,Ki=140nM
Enzymatic activity
Catalytic site (original residue number in PDB) G43 Q48 C91 L92 H133 E134 H137
Catalytic site (residue number reindexed from 1) G43 Q48 C91 L92 H133 E134 H137
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:3pn4, PDBe:3pn4, PDBj:3pn4
PDBsum3pn4
PubMed21629676
UniProtQ9FUZ2|DEF1B_ARATH Peptide deformylase 1B, chloroplastic/mitochondrial (Gene Name=PDF1B)

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