Structure of PDB 1nl4 Chain B Binding Site BS03

Receptor Information
>1nl4 Chain B (length=401) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYSLRPEHARERLQDDSVETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLV
LQREKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIV
ATDVCQFLELCQSPDGGFGGGPGQYPHLAPTYAAVNALCIIGTEEAYNVI
NREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLF
EGTAEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKS
LLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPA
LSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSI
AQHFGSGAMLHDVVMGVPENVLQPTHPVYNIGPDKVIQATTHFLQKPVPG
F
Ligand information
Ligand IDFTL
InChIInChI=1S/C30H23N5/c1-34-21-33-18-27(34)20-35(19-23-7-4-6-22(14-23)16-31)26-13-12-25(17-32)30(15-26)29-11-5-9-24-8-2-3-10-28(24)29/h2-15,18,21H,19-20H2,1H3
InChIKeyIQZCODLAPFPVNS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cn1cncc1CN(Cc2cccc(c2)C#N)c3ccc(c(c3)c4cccc5c4cccc5)C#N
CACTVS 3.341Cn1cncc1CN(Cc2cccc(c2)C#N)c3ccc(C#N)c(c3)c4cccc5ccccc45
ACDLabs 10.04N#Cc5c(c2c1ccccc1ccc2)cc(N(Cc3cccc(C#N)c3)Cc4cncn4C)cc5
FormulaC30 H23 N5
Name4-[(3-CYANO-BENZYL)-(3-METHYL-3H-IMIDAZOL-4-YLMETHYL)-AMINO]-2-NAPHTHALEN-1-YL-BENZONITRILE
ChEMBLCHEMBL27843
DrugBank
ZINCZINC000013489061
PDB chain1nl4 Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1nl4 Novel and Selective Imidazole-containing Biphenyl Inhibitors of Protein Farnesyltransferase
Resolution2.7 Å
Binding residue
(original residue number in PDB)		W102 W106 D297 D359 Y361 H362
Binding residue
(residue number reindexed from 1)		W80 W84 D275 D337 Y339 H340
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.41,IC50=0.39nM
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) H226 R269 K272 D275 C277 Y278 D330 D337 H340
Enzyme Commision number 2.5.1.58: protein farnesyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004311 farnesyltranstransferase 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:0042277 peptide binding
GO:0046872 metal ion binding
Biological Process
GO:0006629 lipid metabolic process
GO:0008283 cell population proliferation
GO:0008284 positive regulation of cell population proliferation
GO:0008285 negative regulation of cell population proliferation
GO:0014070 response to organic cyclic compound
GO:0018343 protein farnesylation
GO:0034097 response to cytokine
GO:0042060 wound healing
GO:0045787 positive regulation of cell cycle
GO:0048144 fibroblast proliferation
GO:0048145 regulation of fibroblast proliferation
GO:0048146 positive regulation of fibroblast proliferation
GO:0051770 positive regulation of nitric-oxide synthase biosynthetic process
Cellular Component
GO:0005875 microtubule associated complex
GO:0005965 protein farnesyltransferase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1nl4, PDBe:1nl4, PDBj:1nl4
PDBsum1nl4
PubMed12657284
UniProtQ02293|FNTB_RAT Protein farnesyltransferase subunit beta (Gene Name=Fntb)

[Back to BioLiP]