2B07

Crystal structure of PTP1B with Tricyclic Thiophene inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb2B07/pdb

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


• Deposited: 2005-09-13 Released: 2005-12-06 
• Deposition Author(s): Moretto, A.F., Kirincich, S.J., Xu, W.X., Smith, M.J., Wan, Z.K., Wilson, D.P., Follows, B.C., Binnun, E., Joseph-McCarthy, D., Foreman, K., Erbe, D.V., Zhang, Y.L., Tam, S.K., Tam, S.Y., Lee, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

Bicyclic and tricyclic thiophenes as protein tyrosine phosphatase 1B inhibitors.

Moretto, A.F., Kirincich, S.J., Xu, W.X., Smith, M.J., Wan, Z.K., Wilson, D.P., Follows, B.C., Binnun, E., Joseph-McCarthy, D., Foreman, K., Erbe, D.V., Zhang, Y.L., Tam, S.K., Tam, S.Y., Lee, J.

(2006) Bioorg Med Chem 14: 2162-2177

• PubMed: 16303309 
• DOI: https://doi.org/10.1016/j.bmc.2005.11.005
• Primary Citation of Related Structures:  
  2AZR, 2B07


• PubMed Abstract: 
  

  A novel pyridothiophene inhibitor of PTP1B was discovered by rational screening of phosphotyrosine mimics at high micromolar concentrations. The potency of this lead compound has been improved significantly by medicinal chemistry guided by X-ray crystallography and molecular modeling. Excellent consistency has been observed between structure-activity relationships and structural information from PTP1B-inhibitor complexes.

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Organizational Affiliation: 

Chemical and Screening Science, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.39 kDa 
• Atom Count: 2,639 
• Modelled Residue Count: 297 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase, non-receptor type 1	A	299	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1, PTP1B 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
598	B [auth A]	6-{[1-(BENZYLSULFONYL)PIPERIDIN-4-YL]AMINO}-3-(CARBOXYMETHOXY)THIENO[3,2-B][1]BENZOTHIOPHENE-2-CARBOXYLIC ACID C25 H24 N2 O7 S3 UEELPALQXUYKFT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
598	BindingDB:  2B07	Ki: 370 (nM) from 1 assay(s)
	PDBBind:  2B07	Ki: 370 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.239	α = 90
b = 88.239	β = 90
c = 104.063	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Moretto, A.F., Kirincich, S.J., Xu, W.X., Smith, M.J., Wan, Z.K., Wilson, D.P., Follows, B.C., Binnun, E., Joseph-McCarthy, D., Foreman, K., Erbe, D.V., Zhang, Y.L., Tam, S.K., Tam, S.Y., Lee, J.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations