Structure of PDB 2vf6 Chain A Binding Site BS01

Receptor Information
>2vf6 Chain A (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYAQEKQDFVQHFSQIVRVLTEPEIGDAIARLKEVLEYNAIGGKYNRGLT
VVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRR
GQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQS
SYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAA
MYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQ
DNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAV
FLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand IDM0N
InChIInChI=1S/C9H12N2O7P2/c12-9(19(13,14)15,20(16,17)18)5-7-6-10-8-3-1-2-4-11(7)8/h1-4,6,12H,5H2,(H2,13,14,15)(H2,16,17,18)
InChIKeyVMMKGHQPQIEGSQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)C(O)(P(=O)(O)O)Cc1cnc2ccccn12
OpenEye OEToolkits 1.5.0c1ccn2c(c1)ncc2CC(O)(P(=O)(O)O)P(=O)(O)O
CACTVS 3.341OC(Cc1cnc2ccccn12)([P](O)(O)=O)[P](O)(O)=O
FormulaC9 H12 N2 O7 P2
Name(1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID);
MINODRONATE;
1-HYDROXY-2-(5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDIN-3-YL)ETHANE-1,1-DIYLDIPHOSPONIC ACID;
(1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YL-ETHYLIDENE)-1,1-BISPHOSPHONIC ACID
ChEMBLCHEMBL319144
DrugBankDB06548
ZINCZINC000003803518
PDB chain2vf6 Chain A Residue 1351 [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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PDB2vf6 Human Fdps Synthase in Complex with Novel Inhibitor
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F99 L100 D103 R112 T167 Q171 K200 T201 Y204 D243 K257
Binding residue
(residue number reindexed from 1)		F86 L87 D90 R99 T154 Q158 K187 T188 Y191 D230 K244
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.52,IC50=3nM
BindingDB: IC50=3nM
Enzymatic activity
Catalytic site (original residue number in PDB) K57 F98 D103 D107 R112 D174 K200 F239 D243 D244
Catalytic site (residue number reindexed from 1) K44 F85 D90 D94 R99 D161 K187 F226 D230 D231
Enzyme Commision number 2.5.1.1: dimethylallyltranstransferase.
2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.
Gene Ontology
Molecular Function
GO:0004659 prenyltransferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
Biological Process
GO:0008299 isoprenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vf6, PDBe:2vf6, PDBj:2vf6
PDBsum2vf6
PubMed
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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