Structure of PDB 5ksx Chain F Binding Site BS03

Receptor Information
>5ksx Chain F (length=339) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYAQEKQDFVQHFSQIVRVLTEGHPEIGDAIARLKEVLEYNAIGGKYNRG
LTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLT
RRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFL
QSSYQTEIGQTLDLLTAPQNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAA
AMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDI
QDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPA
VFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKR
Ligand information
Ligand ID7AM
InChIInChI=1S/C22H21N4O4PS/c1-14-7-9-16(10-8-14)19-12-17-20(23-13-24-22(17)32-19)25-18(21(27)26-31(28,29)30)11-15-5-3-2-4-6-15/h2-10,12-13,18H,11H2,1H3,(H,23,24,25)(H3,26,27,28,29,30)/t18-/m0/s1
InChIKeyFWELKNKHGIBMRD-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(cc1)c2sc3ncnc(N[CH](Cc4ccccc4)C(=O)N[P](O)(O)=O)c3c2
CACTVS 3.385Cc1ccc(cc1)c2sc3ncnc(N[C@@H](Cc4ccccc4)C(=O)N[P](O)(O)=O)c3c2
OpenEye OEToolkits 2.0.5Cc1ccc(cc1)c2cc3c(ncnc3s2)N[C@@H](Cc4ccccc4)C(=O)NP(=O)(O)O
OpenEye OEToolkits 2.0.5Cc1ccc(cc1)c2cc3c(ncnc3s2)NC(Cc4ccccc4)C(=O)NP(=O)(O)O
FormulaC22 H21 N4 O4 P S
Name[[(2~{S})-2-[[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoyl]amino]phosphonic acid
ChEMBLCHEMBL4094213
DrugBank
ZINC
PDB chain5ksx Chain F Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ksx Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		K57 N59 F239 R346 K347 I348 K350
Binding residue
(residue number reindexed from 1)		K46 N48 F227 R334 K335 I336 K338
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.43,IC50=3.7uM
BindingDB: IC50=3700nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5ksx, PDBe:5ksx, PDBj:5ksx
PDBsum5ksx
PubMed28208018
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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