Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 37.91 kDa 
• Atom Count: 2603 
• Residue Count: 295 
• 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)
• 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 

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, 2BGD


• 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P18031  Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS  P18031 GTEx  ENSG00000196396

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
T1D	Kd :  10000   nM  PDBBind
T1D	IC50:  2500   nM  BindingDB
T1D	IC50:  2470   nM  Binding MOAD
T1D	Ki:  2400   nM  BindingDB
T1D	IC50:  2470   nM  BindingDB
T1D	IC50:  4800   nM  BindingDB

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

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
  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