Structure of PDB 4je7 Chain B Binding Site BS01

Receptor Information
>4je7 Chain B (length=189) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPCVGLAA
PQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSN
KKALFFEGCESVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQ
HECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGS
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 chain4je7 Chain B Residue 201 [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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PDB4je7 Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		P46 C47 V48 G49 Q54 R84 E109 G110 C111 E112 R118 W146 R149 H153 E154 H157
Binding residue
(residue number reindexed from 1)		P44 C45 V46 G47 Q52 R82 E107 G108 C109 E110 R116 W144 R147 H151 E152 H155
Annotation score1
Binding affinityMOAD: Kd=395nM
BindingDB: IC50=27nM
Enzymatic activity
Catalytic site (original residue number in PDB) G49 Q54 C111 E112 H153 E154 H157
Catalytic site (residue number reindexed from 1) G47 Q52 C109 E110 H151 E152 H155
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:4je7, PDBe:4je7, PDBj:4je7
PDBsum4je7
PubMed24531459
UniProtQ9FV53|DEF1A_ARATH Peptide deformylase 1A, chloroplastic/mitochondrial (Gene Name=PDF1A)

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