Macromolecule Content

Total Structure Weight: 23.32 kDa
Atom Count: 1706
Residue Count: 183
Unique protein chains: 1

3TJ2

Structure of a novel submicromolar MDM2 inhibitor

DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.308
R-Value Work: 0.223
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TJ2 Query on TJ2 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain F [C] MOL2 format, chain C [A] MOL2 format, chain F [C]	A, 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		Ligand Interaction
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] MOL2 format, chain D [A] MOL2 format, chain E [A]	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TJ2	Ki: 400 nM BindingDB
TJ2	Ki: 700 nM BindingDB
TJ2	Ki: 300 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.308
R-Value Work: 0.223
R-Value Observed: 0.223
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2011-08-23
Released Date: 2012-09-12

Deposition Author(s):

Revision History

Version 1.0: 2012-09-12
Type: Initial release
Version 1.1: 2017-11-08
Changes: Database references, Refinement description

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.