1O5M

Structure of FPT bound to the inhibitor SCH66336


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Tricyclic Farnesyl Protein Transferase Inhibitors: Crystallographic and Calorimetric Studies of Structure-Activity Relationships

Strickland, C.L.Weber, P.C.Windsor, W.T.Wu, Z.Le, H.V.Albanese, M.M.Alvarez, C.S.Cesarz, D.del Rosario, J.Deskus, J.Mallams, A.K.Njoroge, F.G.Piwinski, J.J.Remiszewski, S.Rossman, R.R.Taveras, A.G.Vibulbhan, B.Doll, R.J.Girijavallabhan, V.M.Ganguly, A.K.

(1999) J.Med.Chem. 42: 2125-2135

  • DOI: 10.1021/jm990030g

  • PubMed Abstract: 
  • Crystallographic and thermodynamic studies of farnesyl protein transferase (FPT) complexed with novel tricyclic inhibitors provide insights into the observed SAR for this unique class of nonpeptidic FPT inhibitors. The crystallographic structures rev ...

    Crystallographic and thermodynamic studies of farnesyl protein transferase (FPT) complexed with novel tricyclic inhibitors provide insights into the observed SAR for this unique class of nonpeptidic FPT inhibitors. The crystallographic structures reveal a binding pattern conserved across the mono-, di-, and trihalogen series. In the complexes, the tricycle spans the FPT active site cavity and interacts with both protein atoms and the isoprenoid portion of bound farnesyl diphosphate. An amide carbonyl, common to the tricyclic compounds described here, participates in a water-mediated hydrogen bond to the protein backbone. Ten high-resolution crystal structures of inhibitors complexed with FPT are reported. Included are crystallographic data for FPT complexed with SCH 66336, a compound currently undergoing clinical trials as an anticancer agent (SCH 66336, 4-[2-[4-(3,10-dibromo-8-chloro-6,11-dihydro-5H-benzo[5, 6]cyclohepta[1, 2-b]pyridin-11-yl)-1-piperidinyl]-2-oxoethyl]-1-piperidinecarbo xamide ). Thermodynamic binding parameters show favorable enthalpies of complex formation and small net entropic contributions as observed for 4-[2-[4-(3,10-dibromo-8-chloro-6,11-dihydro-11H-benzo[5, 6]cyclohepta[1, 2-b]pyridin-11-ylidene)-1-piperidinyl]-2-oxoethyl]pyridine N-oxide where DeltaH degrees bind = -12.5 kcal/mol and TDeltaS degrees bind = -1.5 kcal/mol.


    Organizational Affiliation

    Department of Structural Chemistry, Schering-Plough Research Institute, Kenilworth, New Jersey 07033, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase alpha subunit
A
377Rattus norvegicusGene Names: Fnta
EC: 2.5.1.58, 2.5.1.59
Find proteins for Q04631 (Rattus norvegicus)
Go to UniProtKB:  Q04631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase beta subunit
B
437Rattus norvegicusGene 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
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
336
Query on 336

Download SDF File 
Download CCD File 
B
4-{2-[4-(3,10-DIBROMO-8-CHLORO-6,11-DIHYDRO-5H-BENZO[5,6]CYCLOHEPTA[1,2-B]PYRIDIN-11-YL)PIPERIDIN-1-YL]-2-OXOETHYL}PIPERIDINE-1-CARBOXAMIDE
SCH66336
C27 H31 Br2 Cl N4 O2
DHMTURDWPRKSOA-RUZDIDTESA-N
 Ligand Interaction
FPP
Query on FPP

Download SDF File 
Download CCD File 
B
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
336EC50: 100 nM (98) BINDINGDB
336IC50: 1.9 nM BINDINGMOAD
336IC50: 1.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.174 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 171.110α = 90.00
b = 171.110β = 90.00
c = 69.310γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-21
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description