5C5A

Crystal Structure of HDM2 in complex with Nutlin-3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report



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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2AB92Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NUT
Query on NUT

Download Ideal Coordinates 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
C30 H30 Cl2 N4 O4
BDUHCSBCVGXTJM-WUFINQPMSA-N
 Ligand Interaction
IOD
Query on IOD

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

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

Download Ideal Coordinates CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NUTKi:  30   nM  BindingDB
NUTKi:  6.400000095367432   nM  BindingDB
NUTIC50:  18   nM  BindingDB
NUTIC50:  610   nM  BindingDB
NUTKi:  11   nM  BindingDB
NUTIC50:  600   nM  BindingDB
NUTKi:  59   nM  BindingDB
NUTKd:  700   nM  BindingDB
NUTKi:  36   nM  BindingDB
NUTKd:  35   nM  BindingDB
NUTKi:  20   nM  BindingDB
NUTKi:  110   nM  BindingDB
NUTIC50:  88   nM  BindingDB
NUTIC50:  89   nM  BindingDB
NUTIC50:  90   nM  BindingDB
NUTKi:  121   nM  BindingDB
NUTIC50:  100   nM  BindingDB
NUTIC50:  13600   nM  BindingDB
NUTKi:  90   nM  BindingDB
NUTIC50:  61   nM  BindingDB
NUTIC50:  70   nM  BindingDB
NUTIC50:  10   nM  BindingDB
NUTIC50:  180   nM  BindingDB
NUTIC50:  105   nM  BindingDB
NUTKi:  140   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.62α = 90
b = 43.63β = 90.04
c = 52.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXmodel building
PHASERphasing

Structure Validation

View Full Validation Report



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