Structure of PDB 4rxa Chain A Binding Site BS01

Receptor Information
>4rxa Chain A (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRG
LTVVVAFRELVPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTR
RGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQ
SSYQTEIGQTLDLLTAPQNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAA
MYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQ
DNKCSWLVVQCLQRATPEQYQIKENYGQVAVKALYEELDLPAVFLQYEED
SYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand ID3F2
InChIInChI=1S/C32H28N6O2/c39-31(37-27-5-1-3-25(19-27)29-33-15-16-34-29)23-11-7-21(8-12-23)22-9-13-24(14-10-22)32(40)38-28-6-2-4-26(20-28)30-35-17-18-36-30/h1-14,19-20H,15-18H2,(H,33,34)(H,35,36)(H,37,39)(H,38,40)
InChIKeyHOYOJUMMRGKESB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(cc(c1)NC(=O)c2ccc(cc2)c3ccc(cc3)C(=O)Nc4cccc(c4)C5=NCCN5)C6=NCCN6
CACTVS 3.385O=C(Nc1cccc(c1)C2=NCCN2)c3ccc(cc3)c4ccc(cc4)C(=O)Nc5cccc(c5)C6=NCCN6
ACDLabs 12.01O=C(Nc2cc(C1=NCCN1)ccc2)c3ccc(cc3)c4ccc(cc4)C(=O)Nc5cccc(c5)C6=NCCN6
FormulaC32 H28 N6 O2
NameN,N'-bis[3-(4,5-dihydro-1H-imidazol-2-yl)phenyl]biphenyl-4,4'-dicarboxamide;
BPH-1358
ChEMBLCHEMBL3410452
DrugBank
ZINCZINC000001681988
PDB chain4rxa Chain A Residue 1001 [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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PDB4rxa Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K57 N59 R60 L62 T63 V66 F239 D243 G343 K347
Binding residue
(residue number reindexed from 1)		K46 N48 R49 L51 T52 V55 F226 D230 G323 K327
Annotation score1
Binding affinityMOAD: ic50=1.8uM
PDBbind-CN: -logKd/Ki=5.74,IC50=1.8uM
BindingDB: IC50=1.8e+3nM
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) K46 F86 D91 D95 R100 D162 K187 F226 D230 D231
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:4rxa, PDBe:4rxa, PDBj:4rxa
PDBsum4rxa
PubMed25815158
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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