Structure of PDB 2az3 Chain B Binding Site BS01

Receptor Information
>2az3 Chain B (length=151) Species: 2242 (Halobacterium salinarum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYA
EHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGT
IRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVY
E
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 chain2az3 Chain B Residue 1200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2az3 Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K13 H56 F61 L65 R89 T95 L113 G114 N116
Binding residue
(residue number reindexed from 1)		K9 H52 F57 L61 R85 T91 L109 G110 N112
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K13 Y53 N116 H119 E132
Catalytic site (residue number reindexed from 1) K9 Y49 N112 H115 E128
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0009117 nucleotide metabolic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2az3, PDBe:2az3, PDBj:2az3
PDBsum2az3
PubMed16293253
UniProtP61136|NDK_HALSA Nucleoside diphosphate kinase (Gene Name=ndk)

[Back to BioLiP]