Structure of PDB 1s63 Chain B Binding Site BS05

Receptor Information
>1s63 Chain B (length=410) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSPVWSEPLYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFSSYKF
NHLVPRLVLQREKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELL
DEPIPQIVATDVCQFLELCQSPEGGFGGGPGQYPHLAPTYAAVNALCIIG
TEEAYDIINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLT
NIITPDLFEGTAEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKR
ERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRA
LHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTC
YCLSGLSIAQHFGSGAMLHDVVLGVPENALQPTHPVYNIGPDKVIQATTY
FLQKPVPGFE
Ligand information
Ligand ID778
InChIInChI=1S/C22H20ClN5O/c23-19-2-1-3-20(10-19)28-9-8-26(15-22(28)29)14-21-12-25-16-27(21)13-18-6-4-17(11-24)5-7-18/h1-7,10,12,16H,8-9,13-15H2
InChIKeyJNUGFGAVPBYSHF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)Cl)N2CCN(CC2=O)Cc3cncn3Cc4ccc(cc4)C#N
OpenEye OEToolkits 1.5.0c1cc(cc(c1)Cl)N2CC[N@@](CC2=O)Cc3cncn3Cc4ccc(cc4)C#N
CACTVS 3.341Clc1cccc(c1)N2CCN(CC2=O)Cc3cncn3Cc4ccc(cc4)C#N
ACDLabs 10.04N#Cc1ccc(cc1)Cn2c(cnc2)CN4CC(=O)N(c3cccc(Cl)c3)CC4
FormulaC22 H20 Cl N5 O
Name4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE;
L-778,123
ChEMBLCHEMBL279433
DrugBankDB07227
ZINCZINC000053070632
PDB chain1s63 Chain B Residue 3012 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1s63 Crystallographic Analysis Reveals that Anticancer Clinical Candidate L-778,123 Inhibits Protein Farnesyltransferase and Geranylgeranyltransferase-I by Different Binding Modes.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		W102 W106 R202 D297 C299 Y361 H362
Binding residue
(residue number reindexed from 1)		W88 W92 R188 D283 C285 Y347 H348
Annotation score1
Binding affinityMOAD: Ki=0.9nM
PDBbind-CN: -logKd/Ki=9.05,Ki=0.9nM
BindingDB: IC50=2nM
Enzymatic activity
Catalytic site (original residue number in PDB) H248 R291 K294 D297 C299 Y300 D352 D359 H362
Catalytic site (residue number reindexed from 1) H234 R277 K280 D283 C285 Y286 D338 D345 H348
Enzyme Commision number 2.5.1.58: protein farnesyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004659 prenyltransferase activity
GO:0004660 protein farnesyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008318 protein prenyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006629 lipid metabolic process
GO:0018343 protein farnesylation
Cellular Component
GO:0005829 cytosol
GO:0005875 microtubule associated complex
GO:0005965 protein farnesyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1s63, PDBe:1s63, PDBj:1s63
PDBsum1s63
PubMed15248757
UniProtP49356|FNTB_HUMAN Protein farnesyltransferase subunit beta (Gene Name=FNTB)

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