2BED

Structure of FPT bound to inhibitor SCH207736


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Enhanced FTase activity achieved via piperazine interaction with catalytic zinc.

Njoroge, F.G.Vibulbhan, B.Pinto, P.Strickland, C.Bishop, W.R.Nomeir, A.Girijavallabhan, V.

(2006) Bioorg Med Chem Lett 16: 984-988

  • DOI: 10.1016/j.bmcl.2005.10.090
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Benzocycloheptapyridine tricyclic compounds with piperazine or substituted piperidine moieties extending either from the 5- or 6-position of the tricyclic bridgehead exhibited enhanced FTase activity: this resulted from favorable binding of the ligan ...

    Benzocycloheptapyridine tricyclic compounds with piperazine or substituted piperidine moieties extending either from the 5- or 6-position of the tricyclic bridgehead exhibited enhanced FTase activity: this resulted from favorable binding of the ligand nitrogen with the catalytic zinc found in the FTase. A single isomer at C-11 with piperazine adduct extending from the 6-position, compound 24, exhibited excellent FTase activity with IC50 = 0.007 microM, soft agar IC50 = 72 nM, and Rat AUC(PO, 10 mpk) = 4.0 microM x h. X-ray of (-)-[8-chloro-6-(1-piperazinyl)-1H-benzo[5,6]]cyclohepta[1,2-b]pyridine-11-yl]-1-(methylsulfonyl)piperidine 24 bound to Ftase revealed favorable interaction between piperazine nitrogen and catalytic zinc atom.


    Organizational Affiliation

    Schering-Plough Research Institute, 2015 Galloping Hill Road, K-15-3-3545, Kenilworth, NJ 07033, USA. george.njoroge@spcorp.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
A
313Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
Find proteins for Q04631 (Rattus norvegicus)
Go to UniProtKB:  Q04631

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase beta subunit
B
401Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
736
Query on 736

Download CCD File 
B
(11S)-8-CHLORO-11-[1-(METHYLSULFONYL)PIPERIDIN-4-YL]-6-PIPERAZIN-1-YL-11H-BENZO[5,6]CYCLOHEPTA[1,2-B]PYRIDINE
C24 H29 Cl N4 O2 S
ZMGCFGGMTCMSDP-QHCPKHFHSA-N
 Ligand Interaction
FPP
Query on FPP

Download CCD File 
B
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
736IC50:  7   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.02α = 90
b = 174.02β = 90
c = 69.73γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-10-24 
  • Released Date: 2006-08-08 
  • Deposition Author(s): Strickland, C.

Revision History 

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Structure summary