Structure of PDB 4qxs Chain F Binding Site BS02

Receptor Information
>4qxs Chain F (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYN
RGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSS
LTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIEL
FLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLP
IAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIG
TDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELD
LPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand IDWC1
InChIInChI=1S/C21H27NO6P2/c1-13(2)14(3)21-18(12-20(29(23,24)25)30(26,27)28)17-11-16(9-10-19(17)22-21)15-7-5-4-6-8-15/h4-11,13-14,20,22H,12H2,1-3H3,(H2,23,24,25)(H2,26,27,28)/t14-/m0/s1
InChIKeyPCZFJEHMSDBRJQ-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@H](c1c(c2cc(ccc2[nH]1)c3ccccc3)CC(P(=O)(O)O)P(=O)(O)O)C(C)C
CACTVS 3.385CC(C)[CH](C)c1[nH]c2ccc(cc2c1CC([P](O)(O)=O)[P](O)(O)=O)c3ccccc3
CACTVS 3.385CC(C)[C@H](C)c1[nH]c2ccc(cc2c1CC([P](O)(O)=O)[P](O)(O)=O)c3ccccc3
OpenEye OEToolkits 1.7.6CC(C)C(C)c1c(c2cc(ccc2[nH]1)c3ccccc3)CC(P(=O)(O)O)P(=O)(O)O
ACDLabs 12.01O=P(O)(O)C(P(=O)(O)O)Cc2c1cc(ccc1nc2C(C)C(C)C)c3ccccc3
FormulaC21 H27 N O6 P2
Name(2-{2-[(2S)-3-methylbutan-2-yl]-5-phenyl-1H-indol-3-yl}ethane-1,1-diyl)bis(phosphonic acid)
ChEMBL
DrugBank
ZINCZINC000220951016
PDB chain4qxs Chain F Residue 403 [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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PDB4qxs Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K57 N59 R60 S205 F206 F239 D243 K347
Binding residue
(residue number reindexed from 1)		K48 N50 R51 S196 F197 F230 D234 K338
Annotation score1
Binding affinityMOAD: ic50=1.1uM
PDBbind-CN: -logKd/Ki=5.96,IC50=1.1uM
BindingDB: IC50=1100nM
Enzymatic activity
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:4qxs, PDBe:4qxs, PDBj:4qxs
PDBsum4qxs
PubMed25630225
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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