5ZXF

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a

Cheng, X.Y.Su, Z.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A87Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NUT
Query on NUT

Download Ideal Coordinates CCD File 
B [auth A]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
Binding Affinity Annotations 
IDSourceBinding Affinity
NUT BindingDB:  5ZXF Ki: min: 6.4, max: 140 (nM) from 11 assay(s)
Kd: min: 35, max: 700 (nM) from 3 assay(s)
IC50: min: 10, max: 3.00e+4 (nM) from 14 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.575α = 90
b = 43.222β = 90
c = 53.853γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China2016ACA128

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release