3LBK

Structure of human MDM2 protein in complex with a small molecule inhibitor

Structural Biology Knowledgebase: 3LBK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 3LBK

Classification: Ligase

Total Structure Weight: 11717.56

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase Mdm2 A 95 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: p53 binding domain
Mutation: L33E
Gene Name(s): MDM2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K23
Query on K23

A 6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H- imidazol-5-yl]-1H-indole-2-carboxylic acid
C25 H17 Cl2 N3 O2
QZJRNGXHRQJBJH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
K23 Ki: 916 - 920 nM (98) BindingDB

N/A in BindingMoad
Ki: 916 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.207
  • Space Group: P 41 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.46 α = 90.00
b = 60.46 β = 90.00
c = 48.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-01-08
  • Released Date: 2010-03-16
  • Deposition author(s): Popowicz, G.M., Czarna, A., Wolf, S., Holak, T.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4