7OK3

Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor edaGDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors

Goebel, L.Kirschner, T.Koska, S.Rai, A.Janning, P.Maffini, S.Vatheuer, H.Czodrowski, P.Goody, R.S.Mueller, M.P.Rauh, D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRasA170Homo sapiensMutation(s): 4 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt
Find proteins for P01116-2 (Homo sapiens)
Explore P01116-2 
Go to UniProtKB:  P01116-2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116-2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VJ8 (Subject of Investigation/LOI)
Query on VJ8

Download Ideal Coordinates CCD File 
B [auth A]edaGDP
C16 H25 N7 O13 P2
ZYFFWDLDVKYDIX-FRJWGUMJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.4α = 90
b = 73.4β = 90
c = 54.2γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRA 1055/5-1
German Research Foundation (DFG)GermanyGO 284/10-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release