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), 0.240 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201100428
Primary Citation of 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

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]

Binding Affinity Annotations
ID	Source	Binding Affinity
07G	BindingDB: 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 (Depositor), 0.240 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (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

View Full Validation Report

Ligand Structure Quality Assessment

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