6QUV

Crystal Structure of KRAS-G12D in complex with GMP-PCP and compound 15R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.475 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

KRAS Binders Hidden in Nature.

Bergner, A.Cockcroft, X.Fischer, G.Gollner, A.Hela, W.Kousek, R.Mantoulidis, A.Martin, L.J.Mayer, M.Mullauer, B.Siszler, G.Wolkerstorfer, B.Kessler, D.McConnell, D.B.

(2019) Chemistry 25: 12037-12041

  • DOI: 10.1002/chem.201902810
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Natural products have proven to be a rich source of molecular architectures for drugs. Here, an integrated approach to natural product screening is proposed, which uncovered eight new natural product scaffolds for KRAS-the most frequently mutated onc ...

    Natural products have proven to be a rich source of molecular architectures for drugs. Here, an integrated approach to natural product screening is proposed, which uncovered eight new natural product scaffolds for KRAS-the most frequently mutated oncogenic driver in human cancers, which has remained thus far undrugged. The approach combines aspects of virtual screening, fragment-based screening, structure-activity relationships (SAR) by NMR, and structure-based drug discovery to overcome the limitations in traditional natural product approaches. By using our approach, a new "snugness of fit" scoring function and the first crystal-soaking system of the active form of KRAS G12D , the protein-ligand X-ray structures of a tricyclic indolopyrrole fungal alkaloid and an indoloisoquinolinone have been successfully elucidated. The natural product KRAS hits discovered provide fruitful ground for the optimization of highly potent natural-product-based inhibitors of the active form of oncogenic RAS. This integrated approach for screening natural products also holds promise for other "undruggable" targets.


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria.,Present address: F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
170Homo sapiensMutation(s): 1 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GCP
Query on GCP

Download SDF File 
Download CCD File 
A, B
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
JJN
Query on JJN

Download SDF File 
Download CCD File 
B
(6~{a}~{R},11~{b}~{S})-6~{a}-(1,4-dimethylpiperidin-4-yl)-7,11~{b}-dihydro-6~{H}-indolo[2,3-c]isoquinolin-5-one
C22 H25 N3 O
WUVGOCFGNZMOJI-SIKLNZKXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.475 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.440α = 90.00
b = 72.203β = 103.23
c = 54.611γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
AutoPROCdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references