5Z02

Crystal structure of HIS6-tagged Mdm2 with nutlin-3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of HIS6-tagged Mdm2 with nutlin-3a

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A110Homo 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 (Subject of Investigation/LOI)
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:  5Z02 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: 1.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.5α = 90
b = 42.99β = 90
c = 54.53γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BUCCANEERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hubei University of TehnologyChina--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release