Structure of PDB 6n83 Chain F Binding Site BS01

Receptor Information
>6n83 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]
SDVYAQEKQDFVQHFSQIVRVLTEGHPEIGDAIARLKEVLEYNAIGGKYN
RGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSS
LTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIEL
FLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLP
IAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIG
TDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELD
LPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
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 chain6n83 Chain F Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6n83 Chirality-Driven Mode of Binding of alpha-Aminophosphonic Acid-Based Allosteric Inhibitors of the Human Farnesyl Pyrophosphate Synthase (hFPPS).
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N59 R60 S205 F206 F239 Q242 L344
Binding residue
(residue number reindexed from 1)		N50 R51 S196 F197 F230 Q233 L335
Annotation score1
Binding affinityMOAD: ic50=0.54uM
PDBbind-CN: -logKd/Ki=6.27,IC50=0.54uM
Enzymatic activity
Catalytic site (original residue number in PDB) K57 F98 D103 D107 R112 D174 K200 F239 D243 D244
Catalytic site (residue number reindexed from 1) K48 F89 D94 D98 R103 D165 K191 F230 D234 D235
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:6n83, PDBe:6n83, PDBj:6n83
PDBsum6n83
PubMed31577901
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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