1MZC

Co-Crystal Structure Of Human Farnesyltransferase With Farnesyldiphosphate and Inhibitor Compound 33a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Dual Protein Farnesyltransferase-Geranylgeranyltransferase-I Inhibitors as Potential Cancer Chemotherapeutic Agents.

DeSolms, S.J.Ciccarone, T.M.MacTough, S.C.Shaw, A.W.Buser, C.A.Ellis-Hutchings, M.Fernandes, C.Hamilton, K.A.Huber, H.E.Kohl, N.E.Lobell, R.B.Robinson, R.G.Tsou, N.N.Walsh, E.S.Graham, S.L.Beese, L.S.Taylor, J.S.

(2003) J Med Chem 46: 2973-2984

  • DOI: 10.1021/jm020587n
  • Primary Citation of Related Structures:  
    1MZC

  • PubMed Abstract: 
  • A series of novel diaryl ether lactams have been identified as very potent dual inhibitors of protein farnesyltransferase (FTase) and protein geranylgeranyltransferase I (GGTase-I), enzymes involved in the prenylation of Ras. The structure of the complex formed between one of these compounds and FTase has been determined by X-ray crystallography ...

    A series of novel diaryl ether lactams have been identified as very potent dual inhibitors of protein farnesyltransferase (FTase) and protein geranylgeranyltransferase I (GGTase-I), enzymes involved in the prenylation of Ras. The structure of the complex formed between one of these compounds and FTase has been determined by X-ray crystallography. These compounds are the first reported to inhibit the prenylation of the important oncogene Ki-Ras4B in vivo. Unfortunately, doses sufficient to achieve this endpoint were rapidly lethal.


    Organizational Affiliation

    Departments of Medicinal Chemistry and Cancer Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Farnesyltransferase alpha SubunitA382Homo sapiensMutation(s): 0 
Gene Names: FNTA
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49354 (Homo sapiens)
Explore P49354 
Go to UniProtKB:  P49354
PHAROS:  P49354
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Farnesyltransferase beta SubunitB437Homo sapiensMutation(s): 0 
Gene Names: FNTB
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49356 (Homo sapiens)
Explore P49356 
Go to UniProtKB:  P49356
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNE (Subject of Investigation/LOI)
Query on BNE

Download Ideal Coordinates CCD File 
F [auth B]2-[3-(3-ETHYL-1-METHYL-2-OXO-AZEPAN-3-YL)-PHENOXY]-4-[1-AMINO-1-(1-METHYL-1H-IMIDIZOL-5-YL)-ETHYL]-BENZONITRILE
C28 H33 N5 O2
MHNMEERHZSPWFL-NSOVKSMOSA-N
 Ligand Interaction
FPP (Subject of Investigation/LOI)
Query on FPP

Download Ideal Coordinates CCD File 
E [auth B]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FPP BindingDB:  1MZC Kd: 2 (nM) from 1 assay(s)
BNE BindingDB:  1MZC IC50: min: 0.06, max: 5.1 (nM) from 4 assay(s)
EC50: 470 (nM) from 1 assay(s)
Binding MOAD:  1MZC IC50: 0.06 (nM) from 1 assay(s)
PDBBind:  1MZC IC50: 0.06 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
CsucroseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.385α = 90
b = 178.385β = 90
c = 64.579γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary