Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 37908.30 
• Atom Count: 2429 
• Residue Count: 321 
• Unique protein chains: 1

2BGD

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

• DOI: 10.2210/pdb2BGD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.200 
• R-Value Work: 0.164 

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 
• DOI: 10.1016/j.bmcl.2005.03.068
• Primary Citation of Related Structures:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN-TYROSINE PHOSPHATASE NON-RECEPTOR TYPE 1	A	321	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1 (PTP1B) EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens) Go to Gene View: PTPN1 Go to UniProtKB:  P18031

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
T1D	A	5-(4-METHOXYBIPHENYL-3-YL)-1,2,5-THIADIAZOLIDIN-3-ONE 1,1-DIOXIDE C15 H14 N2 O4 S IGXKSKWHHHYBFM-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
T1D	IC50: 2470 - 2500 nM (100) BINDINGDB
T1D	IC50: 2470 nM BINDINGMOAD
T1D	Kd: <10000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.200 
• R-Value Work: 0.164 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 88.908	α = 90.00
b = 88.908	β = 90.00
c = 104.548	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-21 
• Released Date: 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.

Revision History 

• Version 1.0: 2005-05-04
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance
• Version 1.2: 2015-09-16
  Type: Source and taxonomy
• Version 1.3: 2019-07-24
  Type: Data collection