5WHE

KRas G12V/D38P, bound to GppNHp and miniprotein 225-11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Exceptionally high-affinity Ras binders that remodel its effector domain.

McGee, J.H.Shim, S.Y.Lee, S.J.Swanson, P.K.Jiang, S.Y.Durney, M.A.Verdine, G.L.

(2018) J Biol Chem 293: 3265-3280

  • DOI: 10.1074/jbc.M117.816348
  • Primary Citation of Related Structures:  
    5WHA, 5WHB, 5WHD, 5WHE, 5WLB, 5WPL, 5WPM

  • PubMed Abstract: 
  • The Ras proteins are aberrantly activated in a wide range of human cancers, often endowing tumors with aggressive properties and resistance to therapy. Decades of effort to develop direct Ras inhibitors for clinical use have thus far failed, largely because of a lack of adequate small-molecule-binding pockets on the Ras surface ...

    The Ras proteins are aberrantly activated in a wide range of human cancers, often endowing tumors with aggressive properties and resistance to therapy. Decades of effort to develop direct Ras inhibitors for clinical use have thus far failed, largely because of a lack of adequate small-molecule-binding pockets on the Ras surface. Here, we report the discovery of Ras-binding miniproteins from a naïve library and their evolution to afford versions with midpicomolar affinity to Ras. A series of biochemical experiments indicated that these miniproteins bind to the Ras effector domain as dimers, and high-resolution crystal structures revealed that these miniprotein dimers bind Ras in an unprecedented mode in which the Ras effector domain is remodeled to expose an extended pocket that connects two isolated pockets previously found to engage small-molecule ligands. We also report a Ras point mutant that stabilizes the protein in the open conformation trapped by these miniproteins. These findings provide new tools for studying Ras structure and function and present opportunities for the development of both miniprotein and small-molecule inhibitors that directly target the Ras proteins.


    Organizational Affiliation

    Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, Massachusetts 02138 and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA,
B [auth D],
C [auth G],
D [auth J]
170Homo sapiensMutation(s): 2 
Gene Names: KRASKRAS2RASK2
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Miniprotein 225-1135synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
AA [auth J],
M [auth A],
S [auth D],
W [auth G]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth F],
DA [auth F],
N [auth A],
O [auth A],
P [auth A],
CA [auth F],
DA [auth F],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
T [auth D],
U [auth D],
X [auth G],
Y [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth J],
R [auth A],
V [auth D],
Z [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.549α = 90
b = 232.525β = 90.16
c = 48.213γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LustgartenUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2020-01-29
    Changes: Derived calculations