1MZC | pdb_00001mzc

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

• PDB DOI: https://doi.org/10.2210/pdb1MZC/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-07 Released: 2003-07-08 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

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

• PubMed: 12825937 
• DOI: https://doi.org/10.1021/jm020587n
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.95 kDa 
• Atom Count: 6,663 
• Modeled Residue Count: 720 
• Deposited Residue Count: 819 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Farnesyltransferase alpha Subunit	A	382	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000168522

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Farnesyltransferase beta Subunit	B	437	Homo sapiens	Mutation(s): 0  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
PHAROS:  P49356 GTEx:  ENSG00000257365

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNE	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
FPP	E [auth B]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BNE	BindingDB:  1MZC	IC50: min: 0.38, max: 5.1 (nM) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.385	α = 90
b = 178.385	β = 90
c = 64.579	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-08 
Deposition Author(s): 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.

Revision History  

• 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
• Version 2.1: 2024-02-14
  Changes: Data collection, Database references, Refinement description, Structure summary