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 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

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: 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.

Biological Assembly 1  

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: 2,603 
• Modelled Residue Count: 295 
• Deposited Residue Count: 321 
• Unique protein chains: 1

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  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T1D	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
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

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

• 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
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other