Structure of PDB 3nub Chain B Binding Site BS02

Receptor Information
>3nub Chain B (length=358) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEFIDLKNQQARIKDKIDAGIQRVLRHGQYILGPEVTELEDRLADFVGA
KYCISCANGTDALQIVQMALGVGPGDEVITPGFTYVATAETVALLGAKPV
YVDIDPRTYNLDPQLLEAAITPRTKAIIPVSLYGQCADFDAINAIASKYG
IPVIEDAAQSFGASYKGKRSCNLSTVACTSFFPSKPLGCYGDGGAIFTND
DELATAIRQIARHGQDRRYHHIRVGVNSRLDTLQAAILLPKLEIFEEEIA
LRQKVAAEYDLSLKQVGIGTPFIEVNNISVYAQYTVRMDNRESVQASLKA
AGVPTAVHYPIPLNKQPAVADEKAKLPVGDKAATQVMSLPMHPYLDTASI
KIICAALT
Ligand information
Ligand IDUD0
InChIInChI=1S/C25H34N5O22P3/c1-9-17(33)12(11(5-26-9)7-47-53(40,41)42)6-27-15-16(28-10(2)31)24(50-21(19(15)35)23(37)38)51-55(45,46)52-54(43,44)48-8-13-18(34)20(36)22(49-13)30-4-3-14(32)29-25(30)39/h3-6,13,15-16,18-22,24,33-36H,7-8H2,1-2H3,(H,28,31)(H,37,38)(H,43,44)(H,45,46)(H,29,32,39)(H2,40,41,42)/b27-6+/t13-,15+,16+,18-,19-,20-,21-,22+,24+/m0/s1
InChIKeyIGKBPIFLZAFLLV-VUZHIUKYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(=O)N[C@H]1[C@H](O[C@@H]([C@@H](O)[C@@H]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[C@@H]3O[C@H]([C@@H](O)[C@H]3O)N4C=CC(=O)NC4=O
OpenEye OEToolkits 1.7.0Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(C(OC(C2O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O
OpenEye OEToolkits 1.7.0Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H]([C@H](O[C@@H]([C@H]2O)C(=O)O)O[P@](=O)(O)O[P@@](=O)(O)OC[C@H]3[C@@H]([C@@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC4OC(C(=O)O)C(O)C(/N=C/c3c(cnc(c3O)C)COP(=O)(O)O)C4NC(=O)C)O)O
CACTVS 3.370CC(=O)N[CH]1[CH](O[CH]([CH](O)[CH]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O
FormulaC25 H34 N5 O22 P3
Name(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000263620550
PDB chain3nub Chain B Residue 400 [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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PDB3nub Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F4 N58 G59 T60 Y85 A87 D156 A158 Q159 S180 F182 S184 K185 H308 Y309
Binding residue
(residue number reindexed from 1)		F4 N58 G59 T60 Y85 A87 D156 A158 Q159 S180 F182 S184 K185 H308 Y309
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y85 D156 Q159 F182 K185 Y219 R229
Catalytic site (residue number reindexed from 1) Y85 D156 Q159 F182 K185 Y219 R229
Enzyme Commision number 2.6.1.98: UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0006065 UDP-glucuronate biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3nub, PDBe:3nub, PDBj:3nub
PDBsum3nub
PubMed20604544
UniProtQ9HZ76|WBPE_PSEAE UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase (Gene Name=wbpE)

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