5C5A

Crystal Structure of HDM2 in complex with Nutlin-3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.146 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

NMR Molecular Replacement, NMR2

Orts, J.Waelti, M.A.Marsh, M.Vera, L.Gossert, A.D.Guentert, P.Riek, R.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
92Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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

Download SDF File 
Download CCD File 
A, B
4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one
Nutlin 3a
C30 H30 Cl2 N4 O4
BDUHCSBCVGXTJM-WUFINQPMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NUTIC50: 18 - 13600 nM (100) BINDINGDB
NUTKi: 6.4 - 121 nM (100) BINDINGDB
NUTKd: 700 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.146 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.620α = 90.00
b = 43.630β = 90.04
c = 52.670γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
XDSdata reduction
PHENIXrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FEBSSwitzerland--
Lichtenberg program of the Volkswagen FoundationSwitzerland--
Japan Society for the Promotion of Science--

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release