Structure of PDB 3nyt Chain A Binding Site BS01

Receptor Information
>3nyt Chain A (length=359) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEFIDLKNQQARIKDKIDAGIQRVLRHGQYILGPEVTELEDRLADFVGA
KYCISCANGTDALQIVQMALGVGPGDEVITPGFTYVATAETVALLGAKPV
YVDIDPRTYNLDPQLLEAAITPRTKAIIPVSLYGQCADFDAINAIASKYG
IPVIEDAAQSFGASYKGKRSCNLSTVACTSFFPSAPLGCYGDGGAIFTND
DELATAIRQIARHGQDRRYHHIRVGVNSRLDTLQAAILLPKLEIFEEEIA
LRQKVAAEYDLSLKQVGIGTPFIEVNNISVYAQYTVRMDNRESVQASLKA
AGVPTAVHYPIPLNKQPAVADEKAKLPVGDKAATQVMSLPMHPYLDTASI
KIICAALTN
Ligand information
Ligand IDULP
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-/m1/s1
InChIKeyIGKBPIFLZAFLLV-IOECPDIJSA-N
SMILES
SoftwareSMILES
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
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
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
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
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
FormulaC25 H34 N5 O22 P3
Name(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(2R,3S,4R,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 (non-preferred name)
ChEMBL
DrugBank
ZINCZINC000263620549
PDB chain3nyt Chain A Residue 368 [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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PDB3nyt Structural investigation on WlaRG from Campylobacter jejuni: A sugar aminotransferase.
Resolution1.301 Å
Binding residue
(original residue number in PDB)		I5 L7 N58 G59 T60 Y85 A87 D156 A158 Q159 S180 F182 S184 H308 Y309
Binding residue
(residue number reindexed from 1)		I5 L7 N58 G59 T60 Y85 A87 D156 A158 Q159 S180 F182 S184 H308 Y309
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y85 D156 Q159 F182 A185 Y219 R229
Catalytic site (residue number reindexed from 1) Y85 D156 Q159 F182 A185 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:3nyt, PDBe:3nyt, PDBj:3nyt
PDBsum3nyt
PubMed28028852
UniProtQ9HZ76|WBPE_PSEAE UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase (Gene Name=wbpE)

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