Macromolecule Content

Total Structure Weight: 12.93 kDa
Atom Count: 899
Modelled Residue Count: 93
Deposited Residue Count: 108
Unique protein chains: 1

3TU1

Exhaustive Fluorine Scanning towards Potent p53-MDM2 Antagonist

DOI: 10.2210/pdb3TU1/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-09-15 Released: 2011-11-02
Deposition Author(s): Wolf, S., Huang, Y., Koes, D., Popowicz, G.M., Camacho, C.J., Holak, T.A., Doemling, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.245
R-Value Work: 0.205
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Exhaustive Fluorine Scanning toward Potent p53-Mdm2 Antagonists.

Huang, Y., Wolf, S., Koes, D., Popowicz, G.M., Camacho, C.J., Holak, T.A., Domling, A.

(2012) ChemMedChem 7: 49-52

PubMed: 21954050 Search on PubMedSearch on PubMed Central
DOI: 10.1002/cmdc.201100428
Primary Citation of Related Structures:
3TU1

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	108	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
07G Query on 07G Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-(tert-butylamino)-1-(2-carboxy-6-chloro-1H-indol-3-yl)-1-[(3,4-difluorobenzyl)(formyl)amino]-2-oxoethylium C₂₃ H₂₁ Cl F₂ N₃ O₄ SKZKZBKXJCIIQD-UHFFFAOYSA-O		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
07G	Ki: 250 nM Binding MOAD
07G	Ki : 250 nM PDBBind

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.245
R-Value Work: 0.205
R-Value Observed: 0.206
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.95	α = 90
b = 59.25	β = 90
c = 82.95	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2011-09-15
Released Date: 2011-11-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-02
Type: Initial release
Version 1.1: 2012-01-18
Changes: Database references
Version 1.2: 2017-11-08
Changes: 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.