6GJ5

CRYSTAL STRUCTURE OF KRAS G12D (GPPCP) IN COMPLEX WITH 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Drugging an undruggable pocket on KRAS.

Kessler, D.Gmachl, M.Mantoulidis, A.Martin, L.J.Zoephel, A.Mayer, M.Gollner, A.Covini, D.Fischer, S.Gerstberger, T.Gmaschitz, T.Goodwin, C.Greb, P.Haring, D.Hela, W.Hoffmann, J.Karolyi-Oezguer, J.Knesl, P.Kornigg, S.Koegl, M.Kousek, R.Lamarre, L.Moser, F.Munico-Martinez, S.Peinsipp, C.Phan, J.Rinnenthal, J.Sai, J.Salamon, C.Scherbantin, Y.Schipany, K.Schnitzer, R.Schrenk, A.Sharps, B.Siszler, G.Sun, Q.Waterson, A.Wolkerstorfer, B.Zeeb, M.Pearson, M.Fesik, S.W.McConnell, D.B.

(2019) Proc Natl Acad Sci U S A 116: 15823-15829

  • DOI: 10.1073/pnas.1904529116
  • Primary Citation of Related Structures:  
    6GJ5, 6GJ6, 6GJ7, 6GJ8

  • PubMed Abstract: 
  • The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene ...

    The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRAS G12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.


    Organizational Affiliation

    Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria; darryl.mcconnell@boehringer-ingelheim.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA, B170Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
F0N
Query on F0N

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
(3~{S})-3-[2-[(2~{R})-pyrrolidin-2-yl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one
C20 H19 N3 O
ZSGGJAFOTVJSHX-AEFFLSMTSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F0N Binding MOAD:  6GJ5 Kd: 4.40e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.074α = 90
b = 40.043β = 101.14
c = 94.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP50A095103
Austrian Science FundAustria854341

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations