3TJ2 | pdb_00003tj2

Structure of a novel submicromolar MDM2 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3TJ2/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-23 Released: 2012-09-12 
• Deposition Author(s): Wolf, S., Huang, Y., Popowicz, G.M., Goda, S., Holak, T.A., Doemling, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.308 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Ugi Multicomponent Reaction Derived p53-Mdm2 Antagonists

Wolf, S., Huang, Y., Popowicz, G.M., Goda, S., Holak, T.A., Doemling, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.32 kDa 
• Atom Count: 1,706 
• Modeled Residue Count: 183 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B [auth C]	95	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TJ2	C [auth A], F [auth C]	3-{(1S)-2-(tert-butylamino)-1-[(4-chlorobenzyl)(formyl)amino]-2-oxoethyl}-6-chloro-1H-indole-2-carboxylic acid C23 H23 Cl2 N3 O4 ZAOJHZGIRKVCBH-FQEVSTJZSA-N
K	D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TJ2	BindingDB:  3TJ2	Ki: 400 (nM) from 1 assay(s)
		IC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.308 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.44	α = 90
b = 58.88	β = 99.21
c = 49.51	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Wolf, S., Huang, Y., Popowicz, G.M., Goda, S., Holak, T.A., Doemling, A.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references, Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description