Structure of PDB 5jv0 Chain F Binding Site BS01

Receptor Information
>5jv0 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]
DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGK
YNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMD
SSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLI
ELFLQSSYQTEIGQTLDLLTAPNVDLVRFTEKRYKSIVKYKTAFYSFYLP
IAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIG
TDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELD
LPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand IDYL5
InChIInChI=1S/C21H19FN3O3PS/c1-13-5-7-15(8-6-13)18-11-17-20(23-12-24-21(17)30-18)25-19(29(26,27)28)10-14-3-2-4-16(22)9-14/h2-9,11-12,19H,10H2,1H3,(H,23,24,25)(H2,26,27,28)/t19-/m1/s1
InChIKeyASWGUDOBPNZODI-LJQANCHMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(cc1)c2sc3ncnc(N[C@@H](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
ACDLabs 12.01c1c(cccc1F)CC(P(O)(=O)O)Nc2ncnc3c2cc(s3)c4ccc(cc4)C
CACTVS 3.385Cc1ccc(cc1)c2sc3ncnc(N[CH](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
OpenEye OEToolkits 2.0.4Cc1ccc(cc1)c2cc3c(ncnc3s2)N[C@@H](Cc4cccc(c4)F)P(=O)(O)O
OpenEye OEToolkits 2.0.4Cc1ccc(cc1)c2cc3c(ncnc3s2)NC(Cc4cccc(c4)F)P(=O)(O)O
FormulaC21 H19 F N3 O3 P S
Name[(1R)-2-(3-fluorophenyl)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}ethyl]phosphonic acid
ChEMBLCHEMBL4550499
DrugBank
ZINC
PDB chain5jv0 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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PDB5jv0 Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		N59 F206 F239 Q242 L246 L344 K347
Binding residue
(residue number reindexed from 1)		N52 F197 F230 Q233 L237 L335 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:5jv0, PDBe:5jv0, PDBj:5jv0
PDBsum5jv0
PubMed28208018
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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