3FEA

Crystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2 at 1.33A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Human MdmX (HdmX) in Complex with p53 Peptide Analogues Reveal Surprising Conformational Changes

Kallen, J.Goepfert, A.Blechschmidt, A.Izaac, A.Geiser, M.Tavares, G.Ramage, P.Furet, P.Masuya, K.Lisztwan, J.

(2009) J.Biol.Chem. 284: 8812-8821

  • DOI: 10.1074/jbc.M809096200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • p53 tumor suppressor activity is negatively regulated through binding to the oncogenic proteins Hdm2 and HdmX. The p53 residues Leu(26), Trp(23), and Phe(19) are crucial to mediate these interactions. Inhibiting p53 binding to both Hdm2 and HdmX shou ...

    p53 tumor suppressor activity is negatively regulated through binding to the oncogenic proteins Hdm2 and HdmX. The p53 residues Leu(26), Trp(23), and Phe(19) are crucial to mediate these interactions. Inhibiting p53 binding to both Hdm2 and HdmX should be a promising clinical approach to reactivate p53 in the cancer setting, but previous studies have suggested that the discovery of dual Hdm2/HdmX inhibitors will be difficult. We have determined the crystal structures at 1.3 A of the N-terminal domain of HdmX bound to two p53 peptidomimetics without and with a 6-chlorine substituent on the indole (which binds in the same subpocket as Trp(23) of p53). The latter compound is the most potent peptide-based antagonist of the p53-Hdm2 interaction yet to be described. The x-ray structures revealed surprising conformational changes of the binding cleft of HdmX, including an "open conformation" of Tyr(99) and unexpected "cross-talk" between the Trp and Leu pockets. Notably, the 6-chloro p53 peptidomimetic bound with high affinity to both HdmX and Hdm2 (K(d) values of 36 and 7 nm, respectively). Our results suggest that the development of potent dual inhibitors for HdmX and Hdm2 should be feasible. They also reveal possible conformational states of HdmX, which should lead to a better prediction of its interactions with potential biological partners.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. joerg.kallen@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mdm4 protein
A
100Homo sapiensMutation(s): 1 
Gene Names: MDM4 (MDMX)
Find proteins for O15151 (Homo sapiens)
Go to Gene View: MDM4
Go to UniProtKB:  O15151
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-6-Cl-Trp-Glu-Ac3c-Leu-NH2
L, M
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
L, M
NON-POLYMERH2 N

--

6CW
Query on 6CW
L, M
L-PEPTIDE LINKINGC11 H11 Cl N2 O2TRP
AIB
Query on AIB
L, M
L-PEPTIDE LINKINGC4 H9 N O2ALA
1AC
Query on 1AC
L, M
PEPTIDE LINKINGC4 H7 N O2ALA
PM3
Query on PM3
L, M
L-PEPTIDE LINKINGC10 H14 N O5 PPHE
ACE
Query on ACE
L, M
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.193 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 42.249α = 90.00
b = 42.249β = 90.00
c = 70.449γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-11-28 
  • Released Date: 2009-01-27 
  • Deposition Author(s): Kallen, J.

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description