3TU1

Exhaustive Fluorine Scanning towards Potent p53-MDM2 Antagonist

• PDB DOI: https://doi.org/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.

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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 

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 
• DOI: https://doi.org/10.1002/cmdc.201100428
• Primary Citation of Related Structures:  
  3TU1

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Organizational Affiliation: 

Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA.

Biological Assembly 1  

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

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

Macromolecule Content

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

Macromolecules

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
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
07G	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

Binding Affinity Annotations
ID	Source	Binding Affinity
07G	Binding MOAD:  3TU1	Ki: 250 (nM) from 1 assay(s)
	PDBBind:  3TU1	Ki: 250 (nM) from 1 assay(s)

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations