Structure of PDB 3pn3 Chain B Binding Site BS01

Receptor Information
>3pn3 Chain B (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 IDPN3
InChIInChI=1S/C15H22N2O4/c1-15(2,3)21-14(19)16-13(10-17(20)11-18)9-12-7-5-4-6-8-12/h4-8,11,13,20H,9-10H2,1-3H3,(H,16,19)/t13-/m0/s1
InChIKeyWLOCWKYZMRXKHU-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)(C)OC(=O)N[CH](CN(O)C=O)Cc1ccccc1
ACDLabs 12.01O=CN(O)CC(NC(=O)OC(C)(C)C)Cc1ccccc1
OpenEye OEToolkits 1.7.0CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)CN(C=O)O
CACTVS 3.370CC(C)(C)OC(=O)N[C@H](CN(O)C=O)Cc1ccccc1
OpenEye OEToolkits 1.7.0CC(C)(C)OC(=O)NC(Cc1ccccc1)CN(C=O)O
FormulaC15 H22 N2 O4
Nametert-butyl {(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl}carbamate
ChEMBL
DrugBank
ZINCZINC000033977105
PDB chain3pn3 Chain B Residue 194 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3pn3 Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		Y80 V102 P104 R146
Binding residue
(residue number reindexed from 1)		Y80 V102 P104 R146
Annotation score1
Binding affinityMOAD: Ki=400nM
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:3pn3, PDBe:3pn3, PDBj:3pn3
PDBsum3pn3
PubMed21629676
UniProtQ9FUZ2|DEF1B_ARATH Peptide deformylase 1B, chloroplastic/mitochondrial (Gene Name=PDF1B)

[Back to BioLiP]