Structure of PDB 8sxy Chain B Binding Site BS01

Receptor Information
>8sxy Chain B (length=358) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MWVKILSVVGARPQFIKAAAVSRVLRASPGVREVLVHTGQHSQVFFEELE
IPDPDYHLGIGGGTHGQNTGRMLEAIEGVLLKEKPDWVLVYGDTDSTLAG
ALAAVKLHIPVAHVEAGLRSFNRRMPEEINRILTDHASDLLFAPTETAVQ
NLLREGIPENRIHLVGDVMYDAALHYGAKAERKSRILERLGLQAKGYVLA
TIHRAENTDDQERLRVILEALAEVHQEVPVVFPVHPRTRKRAEAFGLGSY
LEKVVALEPVGYLDMVMLEKNARLIVTDSGGVQKEAYFYRVPCVTVREET
EWVELLKAEWNYLAAPQNAKDLALTILHRMRTKGVEIDLYGDGRASQKIS
DFLRKVGI
Ligand information
Ligand IDMJ3
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-ZVWGYSLJSA-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
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
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
FormulaC19 H28 N4 O18 P2
Name(2~{S},3~{S},4~{R},5~{S},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-mannuronic acid
ChEMBL
DrugBank
ZINCZINC000095628035
PDB chain8sxy 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

[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]
PDB8sxy Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
R12 P13 Q14 I16 K17 G97 D98 E120 E132 H208 V265 Y267 M270 S284 G285 G286 E290 W307
Binding residue
(residue number reindexed from 1)
R12 P13 Q14 I16 K17 G92 D93 E115 E127 H203 V260 Y262 M265 S279 G280 G281 E285 W302
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:8sxy, PDBe:8sxy, PDBj:8sxy
PDBsum8sxy
PubMed37660908
UniProtQ72KY0

[Back to BioLiP]