Structure of PDB 4lk3 Chain D Binding Site BS02

Receptor Information
>4lk3 Chain D (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKRILITGGAGFVGSHLTDKLMMDGHEVTVVDNFFTGRKRNVEHWIGHEN
FELINHDVVEPLYIEVDQIYHLASPASPYNPIKTLKTNTIGTLNMLGLAK
RVGARLLLASTSEVYEGKAVAETMCYAYMKQEGVEVRVARIFNTFGPRMH
MNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNV
SSPVNLGNPEEHTILEFAQLIKNLVGSGSEIQFLRKPDIKKAKLMLGWEP
VVPLEEGLNKAIHYFRKELEYQA
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain4lk3 Chain D Residue 502 [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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PDB4lk3 Man o' war mutation in UDP-alpha-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation.
Resolution2.64 Å
Binding residue
(original residue number in PDB)		R272 V273 N276 T288 Y290 Q295 R297 I331
Binding residue
(residue number reindexed from 1)		R155 V156 N159 T171 Y173 Q178 R180 I214
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T202 S203 E204 K235 R272
Catalytic site (residue number reindexed from 1) T111 S112 E113 K118 R155
Enzyme Commision number 4.1.1.35: UDP-glucuronate decarboxylase.
Gene Ontology
Molecular Function
GO:0048040 UDP-glucuronate decarboxylase activity
GO:0070403 NAD+ binding
Biological Process
GO:0042732 D-xylose metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4lk3, PDBe:4lk3, PDBj:4lk3
PDBsum4lk3
PubMed25521717
UniProtQ8NBZ7|UXS1_HUMAN UDP-glucuronic acid decarboxylase 1 (Gene Name=UXS1)

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