Structure of PDB 4l2x Chain F Binding Site BS01

Receptor Information
>4l2x Chain F (length=346) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGK
YNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMD
SSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLI
ELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFY
LPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGK
IGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEE
LDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK
Ligand information
Ligand IDYL2
InChIInChI=1S/C16H17N3O6P2S/c20-26(21,22)16(27(23,24)25)19-14-12-7-13(28-15(12)18-8-17-14)11-5-3-10(4-6-11)9-1-2-9/h3-9,16H,1-2H2,(H,17,18,19)(H2,20,21,22)(H2,23,24,25)
InChIKeyVIGDNIIDHDWALF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)C(Nc1ncnc2sc(cc12)c3ccc(cc3)C4CC4)P(=O)(O)O
CACTVS 3.370O[P](O)(=O)C(Nc1ncnc2sc(cc12)c3ccc(cc3)C4CC4)[P](O)(O)=O
OpenEye OEToolkits 1.7.6c1cc(ccc1c2cc3c(ncnc3s2)NC(P(=O)(O)O)P(=O)(O)O)C4CC4
FormulaC16 H17 N3 O6 P2 S
Name({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)
ChEMBLCHEMBL3087937
DrugBank
ZINCZINC000098209644
PDB chain4l2x Chain F Residue 401 [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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PDB4l2x Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		F99 D103 R112 T167 Q171 K200 T201 D243 K257
Binding residue
(residue number reindexed from 1)		F92 D96 R105 T160 Q164 K193 T194 D236 K250
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.41,IC50=39nM
BindingDB: IC50=115nM
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:4l2x, PDBe:4l2x, PDBj:4l2x
PDBsum4l2x
PubMed23998921
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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