Structure of PDB 8sy0 Chain B Binding Site BS01

Receptor Information
>8sy0 Chain B (length=363) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MWVKILSVVGARPQFIKAAAVSRVLRASPGVREVLVHTGQHYDDNMSQVF
FEELEIPDPDYHLGIGGGTHGQNTGRMLEAIEGVLLKEKPDWVLVYGDTD
STLAGALAAVKLHIPVAHVEAGLRSFNRRMPEEINRILTDHASDLLFAPT
ETAVQNLLREGIPENRIHLVGDVMYDAALHYGAKAERKSRILERLGLQAK
GYVLATIHRAENTDDQERLRVILEALAEVHQEVPVVFPVHPRTRKRAEAF
GLGSYLEKVVALEPVGYLDMVMLEKNARLIVTDSGGVQKEAYFYRVPCVT
VREETEWVELLKAEWNYLAAPQNAKDLALTILHRMRTKGVEIDLYGDGRA
SQKISDFLRKVGI
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 chain8sy0 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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PDB8sy0 Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
R12 P13 Q14 I16 K17 F50 G97 D98 E120 E132 H208 R209 V265 Y267 M270 S284 G285 G286 E290 E306 W307
Binding residue
(residue number reindexed from 1)
R12 P13 Q14 I16 K17 F50 G97 D98 E120 E132 H208 R209 V265 Y267 M270 S284 G285 G286 E290 E306 W307
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:8sy0, PDBe:8sy0, PDBj:8sy0
PDBsum8sy0
PubMed37660908
UniProtQ72KY0

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