6Q9L

HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes.

Kallen, J.Izaac, A.Chau, S.Wirth, E.Schoepfer, J.Mah, R.Schlapbach, A.Stutz, S.Vaupel, A.Guagnano, V.Masuya, K.Stachyra, T.M.Salem, B.Chene, P.Gessier, F.Holzer, P.Furet, P.

(2019) Chemmedchem 14: 1305-1314

  • DOI: 10.1002/cmdc.201900201
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hdm2 (human MDM2) counteracts p53 function by direct binding to p53 and by ubiquitin-dependent p53 protein degradation. Activation of p53 by inhibitors of the p53-Hdm2 interaction is being pursued as a therapeutic strategy in p53 wild-type cancers. I ...

    Hdm2 (human MDM2) counteracts p53 function by direct binding to p53 and by ubiquitin-dependent p53 protein degradation. Activation of p53 by inhibitors of the p53-Hdm2 interaction is being pursued as a therapeutic strategy in p53 wild-type cancers. In addition, HdmX (human MDMX, human MDM4) was also identified as an important therapeutic target to efficiently reactivate p53, and it is likely that dual inhibition of Hdm2 and HdmX is beneficial. Here, we report four new X-ray structures for Hdm2 and five new X-ray structures for HdmX complexes, involving different classes of synthetic compounds. We also reveal the key additive 18-crown-ether, which we have discovered to enable HdmX crystallization and show its stabilization of various Lys-residues. In addition, we report the previously unpublished details of X-ray structure determinations for eight further Hdm2 complexes, including the clinical trial compounds NVP-CGM097 and NVP-HDM201. An analysis of all compound binding modes reveals new and deepened insights into the possible adaptations and structural states of Hdm2 (e.g. flip of F55; flip of Y67; reorientation of H96) and HdmX (e.g. flip of H55; dimer induction), enabling key binding interactions for different compound classes. In order to make comparisons easier, we have used the same numbering for Hdm2 and HdmX. Taken together, these structural insights should prove useful for the design and optimization of further selective and/or dual Hdm2/HdmX inhibitors.


    Organizational Affiliation

    Dr. J. Kallen, A. Izaac, S. Chau, E. Wirth, Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus CH-4002 Basel Switzerland, SWITZERLAND.,Novartis Pharma AG, CBT/NIBR, Fabrikstrasse 2, 4056, Basel, SWITZERLAND.,Dr. K. Masuya, Present address: Peptidream Inc., Menguro, Tokyo, Japan, SWITZERLAND.,Dr. P. Furet, Dr. P. Holzer, Dr. F. Gessier, Dr. R. Mah, Dr. A. Schapbach, Dr. J. Schoepfer, Dr. B. Salem, S. Stutz, Dr. A. Vaupel, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus CH-4002 Basel Switzerland, E-mail:, SWITZERLAND.,Dr. T.M. Stachyra, Dr. P. Chene, Disease Area Oncology, Novartis Institutes for BioMedical Research, Novartis Campus CH-4002 Basel Switzerland, SWITZERLAND.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
96Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HTZ
Query on HTZ

Download SDF File 
Download CCD File 
A, B
[6-chloranyl-3-[3-[[4-chloranyl-2-(hydroxymethyl)phenyl]methyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]-[(3~{S})-3-[3-(dimethylamino)propyl-methyl-amino]pyrrolidin-1-yl]methanone
C36 H40 Cl2 N6 O2
VRHBMXYDRLEJAA-LJAQVGFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.773α = 90.00
b = 87.407β = 90.00
c = 37.141γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-12-18 
  • Released Date: 2019-05-15 
  • Deposition Author(s): Kallen, J.

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-07-24
    Type: Data collection, Database references