Structure of PDB 2v2q Chain B Binding Site BS02

Receptor Information
>2v2q Chain B (length=270) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMIKVLSPAKINLGLWVLGRLPSGYHEILTLYQEIPFYDEIYIREGVLR
VETNIGIPQEENLVYKGLREFERITGIEINYSIFIQKNIPPGAGLGGGSS
NLAVVLKKVNELLGSPLSEEELRELVGSISADAPFFLLGKSAIGRGKGEV
LEPVETEISGKITLVIPQVSSSTGRVYSSLREEHFVTPEYAEEKIQRIIS
GEVEEIENVLGDIARELYPEINEVYRFVEYLGFKPFVSGSGSTVYFFGGA
SEELKKAAKMRGWKVVELEL
Ligand information
Ligand IDNVG
InChIInChI=1S/C19H22N6O5/c20-13-7-8-25(19(29)24-13)18-17(28)16(27)12(30-18)9-21-15(26)6-5-14-22-10-3-1-2-4-11(10)23-14/h1-4,7-8,12,16-18,27-28H,5-6,9H2,(H,21,26)(H,22,23)(H2,20,24,29)/t12-,16+,17+,18+/m0/s1
InChIKeyIHRYIMVLMZNCKA-FCRVUTKVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2c(c1)[nH]c(n2)CCC(=O)NCC3C(C(C(O3)N4C=CC(=NC4=O)N)O)O
OpenEye OEToolkits 1.5.0c1ccc2c(c1)[nH]c(n2)CCC(=O)NC[C@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=NC4=O)N)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CNC(=O)CCc3[nH]c4ccccc4n3)[CH](O)[CH]2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@@H](CNC(=O)CCc3[nH]c4ccccc4n3)[C@@H](O)[C@H]2O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)CNC(=O)CCc3nc4ccccc4n3
FormulaC19 H22 N6 O5
Name4-AMINO-1-(5-{[3-(1H-BENZIMIDAZOL-2-YL)PROPANOYL]AMINO}-5-DEOXY-ALPHA-L-LYXOFURANOSYL)PYRIMIDIN-2(1H)-ONE
ChEMBL
DrugBank
ZINCZINC000016052576
PDB chain2v2q Chain B Residue 1273 [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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PDB2v2q Synthesis and Characterization of Cytidine Derivatives that Inhibit the Kinase Ispe of the Non-Mevalonate Pathway for Isoprenoid Biosynthesis.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y24 H25 I127 S128 A129 K145 T171 Y175
Binding residue
(residue number reindexed from 1)		Y26 H27 I129 S130 A131 K147 T173 Y177
Annotation score1
Binding affinityMOAD: Ki=71.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) K9 D130
Catalytic site (residue number reindexed from 1) K11 D132
Enzyme Commision number 2.7.1.148: 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0050515 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0016310 phosphorylation
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2v2q, PDBe:2v2q, PDBj:2v2q
PDBsum2v2q
PubMed18033714
UniProtO67060|ISPE_AQUAE 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (Gene Name=ispE)

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