Structure of PDB 8syd Chain B Binding Site BS01

Receptor Information
>8syd Chain B (length=371) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLYFQGHMWVKILSVVGARPQFIKAAAVSRVLRASPGVREVLVHTGQHYD
DNMSQVFFEELEIPDPDYHLGIGGGTHGQNTGRMLEAIEGVLLKEKPDWV
LVYGNTDSTLAGALAAVKLHIPVAHVEAGLRSFNRRMPEEINRILTDHAS
DLLFAPTETAVQNLLREGIPENRIHLVGDVMYDAALHYGAKAERKSRILE
RLGLQAKGYVLATIHRAENTDDQERLRVILEALAEVHQEVPVVFPVHPRT
RKRAEAFGLGSYLEKVVALEPVGYLDMVMLEKNARLIVTDSGGVQKEAYF
YRVPCVTVREETEWVELLKAEWNYLAAPQNAKDLALTILHRMRTKGVEID
LYGDGRASQKISDFLRKVGIR
Ligand information
Ligand IDMJL
InChIInChI=1S/C19H28N4O18P2/c1-6(24)20-10-11(21-7(2)25)18(39-15(13(10)28)17(30)31)40-43(35,36)41-42(33,34)37-5-8-12(27)14(29)16(38-8)23-4-3-9(26)22-19(23)32/h3-4,8,10-16,18,27-29H,5H2,1-2H3,(H,20,24)(H,21,25)(H,30,31)(H,33,34)(H,35,36)(H,22,26,32)/t8-,10-,11-,12-,13+,14-,15+,16-,18-/m1/s1
InChIKeyGZLIMKLKXDFTJR-LTMKHLKMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N[CH]1[CH](O)[CH](O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(O)=O
CACTVS 3.385CC(=O)N[C@H]1[C@H](O)[C@H](O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(O)=O
ACDLabs 12.01O=C1C=CN(C(=O)N1)C1OC(COP(=O)(O)OP(=O)(O)OC2OC(C(O)C(NC(C)=O)C2NC(C)=O)C(=O)O)C(O)C1O
OpenEye OEToolkits 2.0.7CC(=O)N[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)C(=O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
OpenEye OEToolkits 2.0.7CC(=O)NC1C(C(OC(C1O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
FormulaC19 H28 N4 O18 P2
Name(2~{S},3~{S},4~{R},5~{R},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic acid;
UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate
ChEMBL
DrugBank
ZINCZINC000095628038
PDB chain8syd Chain B Residue 401 [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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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)
R12 P13 Q14 I16 K17 F50 G97 N98 E120 E132 R136 H208 R209 V265 M270 S284 G285 G286 E290 E306 W307
Binding residue
(residue number reindexed from 1)
R19 P20 Q21 I23 K24 F57 G104 N105 E127 E139 R143 H215 R216 V272 M277 S291 G292 G293 E297 E313 W314
Annotation score2
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

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