Structure of PDB 4jwk Chain A Binding Site BS01

Receptor Information
>4jwk Chain A (length=193) Species: 575584 (Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSNISLIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGIS
GRGNIEGHDVRLLLPMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMN
PGVIRLKTGGGHGGHNGLRDIVPHIGPNFHRLRIGIGHPGSKERVSGHVL
GKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQAMNQINAYKPA
Ligand information
Ligand IDCTN
InChIInChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChIKeyUHDGCWIWMRVCDJ-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
FormulaC9 H13 N3 O5
Name4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE;
CYTIDINE
ChEMBLCHEMBL95606
DrugBankDB02097
ZINCZINC000002583632
PDB chain4jwk Chain A Residue 201 [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]
PDB4jwk The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii
Resolution1.87 Å
Binding residue
(original residue number in PDB)
H22 Y68 M69 N70 N116 L150
Binding residue
(residue number reindexed from 1)
H22 Y68 M69 N70 N116 L150
Annotation score1
Binding affinityMOAD: Kd=5.3nM
PDBbind-CN: -logKd/Ki=8.32,Kd=4.79nM
Enzymatic activity
Catalytic site (original residue number in PDB) H22 N70 D95 N116
Catalytic site (residue number reindexed from 1) H22 N70 D95 N116
Enzyme Commision number 3.1.1.29: peptidyl-tRNA hydrolase.
Gene Ontology
Molecular Function
GO:0004045 aminoacyl-tRNA hydrolase activity
GO:0016787 hydrolase activity
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4jwk, PDBe:4jwk, PDBj:4jwk
PDBsum4jwk
PubMed23844024
UniProtD0C9L6

[Back to BioLiP]