Structure of PDB 1ni1 Chain B Binding Site BS03

Receptor Information

>1ni1 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 ID

2C5

InChI

InChI=1S/C25H17Cl2N5O/c1-32-15-30-13-23(32)24(17-7-5-16(11-28)6-8-17)33-14-22-21(10-19(12-29)25(27)31-22)18-3-2-4-20(26)9-18/h2-10,13,15,24H,14H2,1H3/t24-/m1/s1

InChIKey

JVWHVGIRXILXMU-XMMPIXPASA-N

SMILES

Software	SMILES
ACDLabs 10.04	Clc1cccc(c1)c2cc(C#N)c(Cl)nc2COC(c3cncn3C)c4ccc(C#N)cc4
CACTVS 3.341	Cn1cncc1[C@H](OCc2nc(Cl)c(cc2c3cccc(Cl)c3)C#N)c4ccc(cc4)C#N
OpenEye OEToolkits 1.5.0	Cn1cncc1[C@@H](c2ccc(cc2)C#N)OCc3c(cc(c(n3)Cl)C#N)c4cccc(c4)Cl
CACTVS 3.341	Cn1cncc1[CH](OCc2nc(Cl)c(cc2c3cccc(Cl)c3)C#N)c4ccc(cc4)C#N
OpenEye OEToolkits 1.5.0	Cn1cncc1C(c2ccc(cc2)C#N)OCc3c(cc(c(n3)Cl)C#N)c4cccc(c4)Cl

Formula

C25 H17 Cl2 N5 O

Name

2-CHLORO-5-(3-CHLORO-PHENYL)-6-[(4-CYANO-PHENYL)-(3-METHYL-3H-IMIDAZOL-4-YL)- METHOXYMETHYL]-NICOTINONITRILE

PDB chain

1ni1 Chain B Residue 10 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	1ni1 Discovery of potent imidazole and cyanophenyl containing farnesyltransferase inhibitors with improved oral bioavailability.
Resolution	2.3 Å
Binding residue (original residue number in PDB)	Y93 L96 W106 R202 D297 D359 Y361
Binding residue (residue number reindexed from 1)	Y71 L74 W84 R180 D275 D337 Y339
Annotation score	1
Binding affinity	MOAD: ic50=0.9nM PDBbind-CN: -logKd/Ki=9.05,IC50=0.90nM

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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:1ni1, PDBe:1ni1, PDBj:1ni1
PDBsum	1ni1
PubMed	12699757
UniProt	Q02293\|FNTB_RAT Protein farnesyltransferase subunit beta (Gene Name=Fntb)

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