Structure of PDB 2v2z Chain B Binding Site BS01

Receptor Information
>2v2z 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 IDCDM
InChIInChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1
InChIKeyYFAUKWZNPVBCFF-XHIBXCGHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(CO)(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)O)O
CACTVS 3.341C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N
CACTVS 3.341C[C](O)(CO)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N
ACDLabs 10.04O=P(O)(OCC(O)C(O)(C)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O)O
FormulaC14 H25 N3 O14 P2
Name4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
ChEMBLCHEMBL1231708
DrugBankDB03687
ZINCZINC000008419042
PDB chain2v2z Chain B Residue 1269 [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]
PDB2v2z Characterization of Aquifex Aeolicus 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase -Ligand Recognition in a Template for Antimicrobial Drug Discovery.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		K9 N11 Y24 H25 S128 A129 D130 G172 Y175
Binding residue
(residue number reindexed from 1)		K11 N13 Y26 H27 S130 A131 D132 G174 Y177
Annotation score4
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:2v2z, PDBe:2v2z, PDBj:2v2z
PDBsum2v2z
PubMed18422643
UniProtO67060|ISPE_AQUAE 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (Gene Name=ispE)

[Back to BioLiP]