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BioLiP

Structure of PDB 5ify Chain C Binding Site BS02

Receptor Information
>5ify Chain C (length=289) Species: 269482 (Burkholderia vietnamiensis G4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARKGIILAGGSGTRLYPITHAVSKQLLPVYDKPMIYYPLSTLMIAGIRDV
LIISTPQDTPRFESMLGDGSQWGMNIQYATQPSPDGLAQAFVIGRDFVGN
EPSALILGDNIFYGHDLAKQLERASAKDTGATVFAYHVQDPERYGVVEFD
REFRAISIEEKPAKPRSSYAVTGLYFYDRQVCDIAADIKPSARGELEITD
VNSRYLAAGQLDVELMGRGYAWLDTGTHDSLIEAGTFIATLQKRQGLMVA
CPEEIAYRRNWIDAEQVLKLAQPLAKNAYGQYLRNLLTH
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain5ify Chain C Residue 501 [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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PDB5ify Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2'-Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose
Resolution2.25 Å
Binding residue
(original residue number in PDB)		Y114 G115 D117 A251 E255 I256
Binding residue
(residue number reindexed from 1)		Y113 G114 D116 A250 E254 I255
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.7.24: glucose-1-phosphate thymidylyltransferase.
Gene Ontology
Molecular Function
GO:0008879 glucose-1-phosphate thymidylyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process

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Molecular Function
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Biological Process
External links

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