Structure of PDB 8db5 Chain C Binding Site BS01

Receptor Information
>8db5 Chain C (length=176) Species: 197 (Campylobacter jejuni) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIKFNIEESKILNGVYIITPNKFSDLRGDIWTAFTDEYLSNLVPNGIKFK
HDKFINSHFNVLRGIHGDVKTYKLVTCVYGEVHQVVVDCRKDSPTYLKWE
KFIISPRNQQLILLPPNMGNSHYVSSKEAVYYYKLAYEGEYLDAPDQFTY
AWNDERIAIDWPTNSPILSERDILAM
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8db5 Chain C 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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PDB8db5 C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni .
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K54 R64 H67 D144 R172
Binding residue
(residue number reindexed from 1)		K53 R63 H66 D143 R171
Annotation score1
Enzymatic activity
Enzyme Commision number 5.1.3.13: dTDP-4-dehydrorhamnose 3,5-epimerase.
Gene Ontology
Molecular Function
GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity
GO:0016853 isomerase activity
GO:0016854 racemase and epimerase activity
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:8db5, PDBe:8db5, PDBj:8db5
PDBsum8db5
PubMed36093987
UniProtA0A0S2CFK0

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