Structure of PDB 2v2z Chain B Binding Site BS02

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 IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2v2z Chain B Residue 1270 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		I55 N60 L61 K85 P89 G90 A91 G92 G94 G95 G96 N99
Binding residue
(residue number reindexed from 1)		I57 N62 L63 K87 P91 G92 A93 G94 G96 G97 G98 N101
Annotation score5
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)

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