2BGD

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

PDB DOI: https://doi.org/10.2210/pdb2BGD/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: 2.40 Å
R-Value Free: 0.200
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 37.91 kDa
Atom Count: 2,603
Modelled Residue Count: 295
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

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(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T1D Query on T1D Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-(4-METHOXYBIPHENYL-3-YL)-1,2,5-THIADIAZOLIDIN-3-ONE 1,1-DIOXIDE C₁₅ H₁₄ N₂ O₄ S IGXKSKWHHHYBFM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
T1D	BindingDB: 2BGD	Ki: 2400 (nM) from 1 assay(s)
	BindingDB: 2BGD	IC50: min: 2470, max: 4800 (nM) from 3 assay(s)
	PDBBind: 2BGD	Kd: 1.00e+4 (nM) from 1 assay(s)
	Binding MOAD: 2BGD	IC50: 2470 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.200
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.908	α = 90
b = 88.908	β = 90
c = 104.548	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2015-09-16
Changes: Source and taxonomy
Version 1.3: 2019-07-24
Changes: Data collection

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Help and Resources

2BGD

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)