Structure of PDB 5jv1 Chain F Binding Site BS01

Receptor Information
>5jv1 Chain F (length=336) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYAQEKQDFVQHFSQIVRVLTEHPEIGDAIARLKEVLEYNAIGGKYNRGL
TVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTR
RGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQ
SSYQTEIGQTLDLLTAPNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAM
YMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQD
NKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVF
LQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand IDYL6
InChIInChI=1S/C21H18ClFN3O3PS/c1-12-5-6-14(9-17(12)22)18-10-16-20(24-11-25-21(16)31-18)26-19(30(27,28)29)8-13-3-2-4-15(23)7-13/h2-7,9-11,19H,8H2,1H3,(H,24,25,26)(H2,27,28,29)/t19-/m1/s1
InChIKeyZSPBSSJYWQDARC-LJQANCHMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4Cc1ccc(cc1Cl)c2cc3c(ncnc3s2)NC(Cc4cccc(c4)F)P(=O)(O)O
CACTVS 3.385Cc1ccc(cc1Cl)c2sc3ncnc(N[C@@H](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
ACDLabs 12.01c1c(Cl)c(C)ccc1c2cc3c(ncnc3s2)NC(Cc4cc(F)ccc4)P(O)(=O)O
OpenEye OEToolkits 2.0.4Cc1ccc(cc1Cl)c2cc3c(ncnc3s2)N[C@@H](Cc4cccc(c4)F)P(=O)(O)O
CACTVS 3.385Cc1ccc(cc1Cl)c2sc3ncnc(N[CH](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
FormulaC21 H18 Cl F N3 O3 P S
Name[(1R)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl)ethyl]phosphonic acid
ChEMBLCHEMBL4515661
DrugBank
ZINC
PDB chain5jv1 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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PDB5jv1 Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K57 N59 R60 S205 F206 F239 Q242 D243
Binding residue
(residue number reindexed from 1)		K45 N47 R48 S191 F192 F225 Q228 D229
Annotation score1
Binding affinityMOAD: ic50=0.86uM
PDBbind-CN: -logKd/Ki=6.07,IC50=0.86uM
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:5jv1, PDBe:5jv1, PDBj:5jv1
PDBsum5jv1
PubMed28208018
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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