Structure of PDB 2vf3 Chain B Binding Site BS01

Receptor Information
>2vf3 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 IDGVS
InChIInChI=1S/C17H22N4O6S/c1-2-27-14(22)8-17(10-26-11-17)21-9-12(15(18)20-16(21)23)4-3-7-19-28(24,25)13-5-6-13/h9,13,19H,2,5-8,10-11H2,1H3,(H2,18,20,23)
InChIKeyMIAWQMZUJQYSPX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCOC(=O)CC1(COC1)N2C=C(C(=NC2=O)N)C#CCNS(=O)(=O)C3CC3
ACDLabs 10.04O=S(=O)(NCC#CC=1C(=NC(=O)N(C=1)C2(COC2)CC(=O)OCC)N)C3CC3
CACTVS 3.341CCOC(=O)CC1(COC1)N2C=C(C#CCN[S](=O)(=O)C3CC3)C(=NC2=O)N
FormulaC17 H22 N4 O6 S
Nameethyl {3-[4-amino-5-{3-[(cyclopropylsulfonyl)amino]prop-1-yn-1-yl}-2-oxopyrimidin-1(2H)-yl]oxetan-3-yl}acetate
ChEMBL
DrugBank
ZINCZINC000058650720
PDB chain2vf3 Chain B Residue 1269 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vf3 Inhibitors of the Kinase Ispe: Structure-Activity Relationships and Co-Crystal Structure Analysis.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N11 Y24 H25 Y31 D130 K145 Y175 G237
Binding residue
(residue number reindexed from 1)		N13 Y26 H27 Y33 D132 K147 Y177 G239
Annotation score1
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:2vf3, PDBe:2vf3, PDBj:2vf3
PDBsum2vf3
PubMed18633530
UniProtO67060|ISPE_AQUAE 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (Gene Name=ispE)

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