Structure of PDB 2y0d Chain A Binding Site BS01

Receptor Information
>2y0d Chain A (length=455) Species: 292 (Burkholderia cepacia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMNLTIIGSGKVGLVTGACLADIGHDVFCLDVDQAKIDILNNGGVPIHEP
GLKEVIARNRSAGRLRFSTDIEAAVAHGDVQFIAVGTPPDESADLQYVLA
AARNIGRYMTGFKVIVDKSTVPVGTAERVRAAVAEELAKRGGDQMFSVVS
NPEFLKEGAAVDDFTRPDRIVIGCDDDVPGERARELMKKLYAPFNRNHER
TLYMDVRSAEFTKYAANAMLATRISFMNELANLADRFGADIEAVRRGIGS
DPRIGYHFLYAGCGYGGSCFPKDVEALIRTADEHGQSLQILKAVSSVNAT
QKRVLADKIVARFGEDLTGRTFAIWGLAFKPNTDDMREAPSRELIAELLS
RGARIAAYDPVAQEEARRVIALDLADHPSWLERLSFVDDEAQAARDADAL
VIVTEWKIFKSPDFVALGRLWKTPVIFDGRNLYEPETMSEQGIEYHPIGR
PGSRQ
Ligand information
Ligand IDUGA
InChIInChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1
InChIKeyHDYANYHVCAPMJV-LXQIFKJMSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O)O)O)O)O
CACTVS 3.341O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)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
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
FormulaC15 H22 N2 O18 P2
NameURIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID;
UDP-GLUCURONIC ACID
ChEMBLCHEMBL228057
DrugBankDB03041
ZINCZINC000008215691
PDB chain2y0d Chain A Residue 500 [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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PDB2y0d Structure of Burkholderia Cepacia Udp-Glucose Dehydrogenase (Ugd) Bcec and Role of Tyr10 in Final Hydrolysis of Ugd Thioester Intermediate.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		E154 F155 L156 E158 K214 N218 I225 F259 Y261 Y266 C270 F271 F330 K331
Binding residue
(residue number reindexed from 1)		E153 F154 L155 E157 K213 N217 I224 F258 Y260 Y265 C269 F270 F329 K330
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T121 E158 K214 N218 C270 D274
Catalytic site (residue number reindexed from 1) T120 E157 K213 N217 C269 D273
Enzyme Commision number 1.1.1.22: UDP-glucose 6-dehydrogenase.
Gene Ontology
Molecular Function
GO:0003979 UDP-glucose 6-dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0006065 UDP-glucuronate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2y0d, PDBe:2y0d, PDBj:2y0d
PDBsum2y0d
PubMed21602353
UniProtC9E261

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