6I3S

Crystal structure of MDM2 in complex with compound 13.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Targeted Synthesis of Complex Spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-ones by Intramolecular Cyclization of Azomethine Ylides: Highly Potent MDM2-p53 Inhibitors.

Gollner, A.Weinstabl, H.Fuchs, J.E.Rudolph, D.Garavel, G.Hofbauer, K.S.Karolyi-Oezguer, J.Gmaschitz, G.Hela, W.Kerres, N.Grondal, E.Werni, P.Ramharter, J.Broeker, J.McConnell, D.B.

(2019) ChemMedChem 14: 88-93


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A
94Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
H28
Query on H28

Download SDF File 
Download CCD File 
A
(3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione
C23 H18 Cl2 F N3 O2
ZWMAKFAKGSTVDL-QPXQOZNCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.064α = 90.00
b = 56.064β = 90.00
c = 105.119γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-11-07 
  • Released Date: 2018-12-19 
  • Deposition Author(s): Bader, G., Kessler, D.

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references
  • Version 1.3: 2019-03-06
    Type: Data collection