4IPF

The 1.7A crystal structure of humanized Xenopus MDM2 with RO5045337

Structural Biology Knowledgebase: 4IPF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IPF

Classification: LIGASE / ANTAGONIST

Total Structure Weight: 10751.41

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase Mdm2 A 85 Xenopus laevis EC#: 6.3.2 IUBMB
Fragment: UNP RESIDUES 21-105
Mutation: I50L, P92H, L95I
Gene Name(s): mdm2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1F0
Query on 1F0

A [(4S,5R)-2-(4-tert-butyl-2-ethoxyphenyl)- 4,5-bis(4-chlorophenyl)-4,5-dimethyl-4,5- dihydro-1H-imidazol-1-yl]{4-[3-(methylsulfonyl)propyl]piperazin- 1-yl}methanone
RG7112, (Synonym)
C38 H48 Cl2 N4 O4 S
QBGKPEROWUKSBK-QPPIDDCLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1F0 N/A in BindingDB
IC50: 18 nM  BindingMOAD
IC50: 18 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.208
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 43.08 α = 90.00
b = 67.49 β = 90.00
c = 66.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-09
  • Released Date: 2013-02-20
  • Deposition author(s): Graves, B.J., Lukacs, C., Kammlott, R.U., Crowther, R.

Revision History

  • 2013-04-24
    Type: Citation | Details: Citation update