6Q9Y

HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; 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: 1.20 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Hdm2 (human MDM2, human double minute 2 homologue) 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 str ...

    Hdm2 (human MDM2, human double minute 2 homologue) 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. Herein we report four new X-ray structures for Hdm2 and five new X-ray structures for HdmX complexes, involving different classes of synthetic compounds (including the worldwide highest resolutions for Hdm2 and HdmX, at 1.13 and 1.20 Å, respectively). We also reveal the key additive 18-crown-ether, which we 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 In addition, we report the previously unpublished details of X-ray structure determinations for eight further Hdm2 complexes, including the clinical trial compounds NVP-CGM097 and NVP-HDM201.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 insight 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. To facilitate comparisons, we used the same numbering for Hdm2 (as in Q00987) and HdmX (as in O15151, but minus 1). Taken together, these structural insights should prove useful for the design and optimization of further selective and/or dual Hdm2/HdmX inhibitors.


    Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Mdm4
A, B
100Homo sapiensMutation(s): 1 
Gene Names: MDM4MDMX
Find proteins for O15151 (Homo sapiens)
Go to UniProtKB:  O15151
NIH Common Fund Data Resources
PHAROS  O15151
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HRQ
Query on HRQ

Download CCD File 
A, B
7-methoxy-~{N}-[(3~{S})-1-(4-methylphenyl)pyrrolidin-3-yl]-1~{H}-indole-3-carboxamide
C21 H23 N3 O2
GMGMKERXGPBQDO-HNNXBMFYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.492α = 90
b = 42.426β = 90
c = 107.421γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references