Structure of PDB 6n82 Chain F Binding Site BS02

Receptor Information
>6n82 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 IDYF7
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-/m0/s1
InChIKeyZSPBSSJYWQDARC-IBGZPJMESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1ccc(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
OpenEye OEToolkits 2.0.6Cc1ccc(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
ACDLabs 12.01c1c(Cl)c(C)ccc1c2sc3c(c2)c(ncn3)NC(Cc4cccc(c4)F)P(O)(O)=O
FormulaC21 H18 Cl F N3 O3 P S
Name[(1S)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-(3-fluorophenyl)ethyl]phosphonic acid
ChEMBLCHEMBL4516343
DrugBank
ZINC
PDB chain6n82 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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PDB6n82 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)		L315 E318 Y322 A345 R346 Y349 K350
Binding residue
(residue number reindexed from 1)		L306 E309 Y313 A336 R337 Y340 K341
Annotation score1
Binding affinityMOAD: ic50=1.1uM
PDBbind-CN: -logKd/Ki=5.96,IC50=1.1uM
BindingDB: IC50=860nM
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) K50 F91 D96 D100 R105 D167 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:6n82, PDBe:6n82, PDBj:6n82
PDBsum6n82
PubMed31577901
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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