4PZY

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report



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: 10.1007/s10858-014-9849-8
  • Structures With Same Primary Citation

  • 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 identifyin ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
K-RasA, B170Homo sapiensMutation(s): 3 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS  P01116
GTEx  ENSG00000133703
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
2XR
Query on 2XR
Download CCD File 
B
2-chloro-1-(1H-indol-3-yl)ethanone
C10 H8 Cl N O
LLZQFAXTCYDVTR-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.101α = 90
b = 55.964β = 90
c = 120.761γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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