3TU1 | pdb_00003tu1

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.245 (Depositor), 0.243 (DCC)
R-Value Work:
0.205 (Depositor), 0.208 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201100428
Primary Citation Related Structures:
3TU1

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D 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)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987 Go to UniProtKB: Q00987
PHAROS: Q00987 GTEx: ENSG00000135679
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00987
Sequence Annotations 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] mmCIF format, chain B [auth A]	B [auth A]	3-[(1S)-2-(tert-butylamino)-1-{N-[(3,4-difluorophenyl)methyl]formamido}-2-oxoethyl]-6-chloro-1H-indole-2-carboxylic acid C₂₃ H₂₂ Cl F₂ N₃ O₄ AGRQHAQMUFKJFC-FQEVSTJZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.245 (Depositor), 0.243 (DCC)
R-Value Work: 0.205 (Depositor), 0.208 (DCC)
R-Value Observed: 0.206 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

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
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations
Version 2.0: 2024-05-29
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary