1S64

Rat protein geranylgeranyltransferase type-I complexed with L-778,123 and a sulfate anion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystallographic Analysis Reveals that Anticancer Clinical Candidate L-778,123 Inhibits Protein Farnesyltransferase and Geranylgeranyltransferase-I by Different Binding Modes.

Reid, T.S.Long, S.B.Beese, L.S.

(2004) Biochemistry 43: 9000-9008

  • DOI: https://doi.org/10.1021/bi049280b
  • Primary Citation of Related Structures:  
    1S63, 1S64

  • PubMed Abstract: 

    Many signal transduction proteins that control growth, differentiation, and transformation, including Ras GTPase family members, require the covalent attachment of a lipid group by protein farnesyltransferase (FTase) or protein geranylgeranyltransferase type-I (GGTase-I) for proper function and for the transforming activity of oncogenic mutants. FTase inhibitors are a new class of potential cancer therapeutics under evaluation in human clinical trials. Here, we present crystal structures of the clinical candidate L-778,123 complexed with mammalian FTase and complexed with the related GGTase-I enzyme. Although FTase and GGTase-I have very similar active sites, L-778,123 adopts different binding modes in the two enzymes; in FTase, L-778,123 is competitive with the protein substrate, whereas in GGTase-I, L-778,123 is competitive with the lipid substrate and inhibitor binding is synergized by tetrahedral anions. A comparison of these complexes reveals that small differences in protein structure can dramatically affect inhibitor binding and selectivity. These structures should facilitate the design of more specific inhibitors toward FTase or GGTase-I. Finally, the binding of a drug and anion together could be applicable for developing new classes of inhibitors.


  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
A, C, E, G, I
A, C, E, G, I, K
377Rattus norvegicusMutation(s): 0 
Gene Names: FNTA
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type I beta subunit
B, D, F, H, J
B, D, F, H, J, L
377Rattus norvegicusMutation(s): 0 
Gene Names: PGGT1B
EC: 2.5.1.59
UniProt
Find proteins for P53610 (Rattus norvegicus)
Explore P53610 
Go to UniProtKB:  P53610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53610
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
778
Query on 778

Download Ideal Coordinates CCD File 
FA [auth H]
LA [auth J]
O [auth B]
RA [auth L]
U [auth D]
FA [auth H],
LA [auth J],
O [auth B],
RA [auth L],
U [auth D],
Z [auth F]
4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE
C22 H20 Cl N5 O
JNUGFGAVPBYSHF-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
AA [auth F]
GA [auth H]
MA [auth J]
P [auth B]
SA [auth L]
AA [auth F],
GA [auth H],
MA [auth J],
P [auth B],
SA [auth L],
V [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth H]
KA [auth J]
N [auth B]
QA [auth L]
T [auth D]
EA [auth H],
KA [auth J],
N [auth B],
QA [auth L],
T [auth D],
Y [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth H]
IA [auth J]
M [auth B]
OA [auth L]
R [auth D]
CA [auth H],
IA [auth J],
M [auth B],
OA [auth L],
R [auth D],
W [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
HA [auth I]
JA [auth J]
NA [auth K]
BA [auth G],
DA [auth H],
HA [auth I],
JA [auth J],
NA [auth K],
PA [auth L],
Q [auth C],
S [auth D],
X [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
778 PDBBind:  1S64 Ki: 4 (nM) from 1 assay(s)
BindingDB:  1S64 IC50: min: 2, max: 2000 (nM) from 8 assay(s)
EC50: 6800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 271.153α = 90
b = 268.681β = 131.55
c = 184.622γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description