2BGE

Structure-based design of Protein Tyrosine Phosphatase-1B Inhibitors

PDB DOI: https://doi.org/10.2210/pdb2BGE/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-12-21 Released: 2005-05-04
Deposition Author(s): Black, E., Breed, J., Breeze, A.L., Embrey, K., Garcia, R., Gero, T.W., Godfrey, L., Kenny, P.W., Morley, A.D., Minshull, C.A., Pannifer, A.D., Read, J., Rees, A., Russell, D.J., Toader, D., Tucker, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.245
R-Value Work: 0.218

wwPDB Validation 3D Report Full Report

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

Literature

Structure-Based Design of Protein Tyrosine Phosphatase-1B Inhibitors

Black, E., Breed, J., Breeze, A.L., Embrey, K., Garcia, R., Gero, T.W., Godfrey, L., Kenny, P.W., Morley, A.D., Minshull, C.A., Pannifer, A.D., Read, J., Rees, A., Russell, D.J., Toader, D., Tucker, J.

(2005) Bioorg Med Chem Lett 15: 2503

PubMed: 15863305 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.03.068
Primary Citation of Related Structures:
2BGD, 2BGE

PubMed Abstract:
Using structure-based design, a new class of inhibitors of protein tyrosine phosphatase-1B (PTP1B) has been identified, which incorporate the 1,2,5-thiadiazolidin-3-one-1,1-dioxide template.

Organizational Affiliation

AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

Macromolecule Content

Total Structure Weight: 37.58 kDa
Atom Count: 2,815
Modelled Residue Count: 298
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN-TYROSINE PHOSPHATASE NON-RECEPTOR TYPE 1	A	321	Homo sapiens	Mutation(s): 0 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031 Go to UniProtKB: P18031
PHAROS: P18031 GTEx: ENSG00000196396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T2D Query on T2D Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1,2,5-THIADIAZOLIDIN-3-ONE-1,1-DIOXIDE C₈ H₈ N₂ O₃ S LDCZCUKQWRZSDT-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
T2D	Binding MOAD: 2BGE	IC50: 1.61e+6 (nM) from 1 assay(s)
	BindingDB: 2BGE	IC50: min: 1.60e+6, max: 1.61e+6 (nM) from 2 assay(s)
	PDBBind: 2BGE	IC50: 1.60e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.245
R-Value Work: 0.218
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.012	α = 90
b = 89.012	β = 90
c = 104.71	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-05-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-05-04
Type: Initial release
Version 1.1: 2015-10-07
Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance