4PZZ

Second-site screening of K-Ras in the presence of covalently attached first-site ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

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Ligand Structure Quality Assessment 


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Literature

A method for the second-site screening of K-Ras in the presence of a covalently attached first-site ligand.

Sun, Q.Phan, J.Friberg, A.R.Camper, D.V.Olejniczak, E.T.Fesik, S.W.

(2014) J Biomol NMR 60: 11-14

  • DOI: https://doi.org/10.1007/s10858-014-9849-8
  • Primary Citation of Related Structures:  
    4PZY, 4PZZ, 4Q01, 4Q02, 4Q03

  • PubMed Abstract: 

    K-Ras is a well-validated cancer target but is considered to be "undruggable" due to the lack of suitable binding pockets. We previously discovered small molecules that bind weakly to K-Ras but wanted to improve their binding affinities by identifying ligands that bind near our initial hits that we could link together. Here we describe an approach for identifying second site ligands that uses a cysteine residue to covalently attach a compound for tight binding to the first site pocket followed by a fragment screen for binding to a second site. This approach could be very useful for targeting Ras and other challenging drug targets.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K-Ras170Homo sapiensMutation(s): 3 
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
2XO
Query on 2XO

Download Ideal Coordinates CCD File 
D [auth A]1H-benzimidazol-2-ylmethanethiol
C8 H8 N2 S
XGIDEUICZZXBFQ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.076α = 90
b = 41.063β = 90
c = 91.678γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release