Structure of PDB 2vbu Chain A Binding Site BS01

Receptor Information
>2vbu Chain A (length=131) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDRE
FDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYH
SSEIIEIIAPMKLREQFNLKDGDVIKILIKG
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)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)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain2vbu Chain A Residue 1133 [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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PDB2vbu A Ctp-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G14 G16 G18 R19 Y40 G42 T43 L44 N45 M112 K113 L114 R115
Binding residue
(residue number reindexed from 1)		G13 G15 G17 R18 Y39 G41 T42 L43 N44 M111 K112 L113 R114
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.161: CTP-dependent riboflavin kinase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0008531 riboflavin kinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0009231 riboflavin biosynthetic process
GO:0009398 FMN biosynthetic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vbu, PDBe:2vbu, PDBj:2vbu
PDBsum2vbu
PubMed18073108
UniProtQ60365|RIFK_METJA Riboflavin kinase (Gene Name=ribK)

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