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 

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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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
K-RasA, B170Homo sapiensMutation(s): 3 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
2XR
Query on 2XR
Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]		2-chloro-1-(1H-indol-3-yl)ethanone
C10 H8 Cl N O
LLZQFAXTCYDVTR-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
F [auth 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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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