Structure of PDB 8syd Chain A Binding Site BS02

Receptor Information
>8syd Chain A (length=360) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MWVKILSVVGARPQFIKAAAVSRVLRASPGVREVLVHTGQHYDDNMSQVF
FEELEIPDPDYHLGIGGGTHGQNTGRMLEAIEGVLLKEKPDWVLVYGNTD
STLAGALAAVKLHIPVAHVEAGLRSFNRRMPEEINRILTDHASDLLFAPT
ETAVQNLLREGIPENRIHLVGDVMYDAALHYGAKAERKSRILERLGLQAK
GYVLATIHRAENTDDQERLRVILEALAEVHQEVPVVFPVHPRTRKRAEAF
GLGSYLEKVVALEPVGYLDMVMLEKNARLIVTDSGGVQKEAYFYRVPCVT
VREETEWVELLKAEWNYLAAPQNAKDLALTILHRMRTKGVEIDLYGDGRA
SQKISDFLRK
Ligand information
Ligand IDUD1
InChIInChI=1S/C17H27N3O17P2/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)36-39(31,32)37-38(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12-,13-,14-,15-,16-/m1/s1
InChIKeyLFTYTUAZOPRMMI-CFRASDGPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
CACTVS 3.341CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
FormulaC17 H27 N3 O17 P2
NameURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
ChEMBLCHEMBL388154
DrugBankDB03397
ZINCZINC000008551100
PDB chain8syd Chain A Residue 402 [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]
PDB8syd Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		P13 Q40 H41 Y42 D43 G67 T99 D100 E132 H208 R209 H240 P241 R242 K245
Binding residue
(residue number reindexed from 1)		P13 Q40 H41 Y42 D43 G67 T99 D100 E132 H208 R209 H240 P241 R242 K245
Annotation score3
Enzymatic activity
Enzyme Commision number 5.1.3.14: UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0008761 UDP-N-acetylglucosamine 2-epimerase activity
GO:0016853 isomerase activity

View graph for
Molecular Function
External links
PDB RCSB:8syd, PDBe:8syd, PDBj:8syd
PDBsum8syd
PubMed37660908
UniProtQ72KY0

[Back to BioLiP]