Structure of PDB 8syd Chain B Binding Site BS02

Receptor Information

>8syd Chain B (length=371) Species: 262724 (Thermus thermophilus HB27)

NLYFQGHMWVKILSVVGARPQFIKAAAVSRVLRASPGVREVLVHTGQHYD
DNMSQVFFEELEIPDPDYHLGIGGGTHGQNTGRMLEAIEGVLLKEKPDWV
LVYGNTDSTLAGALAAVKLHIPVAHVEAGLRSFNRRMPEEINRILTDHAS
DLLFAPTETAVQNLLREGIPENRIHLVGDVMYDAALHYGAKAERKSRILE
RLGLQAKGYVLATIHRAENTDDQERLRVILEALAEVHQEVPVVFPVHPRT
RKRAEAFGLGSYLEKVVALEPVGYLDMVMLEKNARLIVTDSGGVQKEAYF
YRVPCVTVREETEWVELLKAEWNYLAAPQNAKDLALTILHRMRTKGVEID
LYGDGRASQKISDFLRKVGIR

Ligand information

• Ligand ID: UD1
• InChI: InChI=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
• InChIKey: LFTYTUAZOPRMMI-CFRASDGPSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=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 3.341: CC(=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 10.04: O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
  CACTVS 3.341: CC(=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 1.5.0: CC(=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
• Formula: C17 H27 N3 O17 P2
• Name: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
• ChEMBL: CHEMBL388154
• DrugBank: DB03397
• ZINC: ZINC000008551100
• PDB chain: 8syd Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8syd Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
• Resolution: 2.2 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): P20 Q47 H48 Y49 D50 G74 T106 D107 E139 H215 R216 H247 P248 R249 K252
• Annotation score: 3

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

External links

• PDB: RCSB:8syd, PDBe:8syd, PDBj:8syd
• PDBsum: 8syd
• PubMed: 37660908
• UniProt: Q72KY0