Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.89 kDa 
• Atom Count: 2509 
• Residue Count: 289 
• Unique protein chains: 1

1Q6J

THE STRUCTURE OF PHOSPHOTYROSINE PHOSPHATASE 1B IN COMPLEX WITH COMPOUND 2

• DOI: 10.2210/pdb1Q6J/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-08-13 Released: 2003-09-30 
• Deposition Author(s): Scapin, G., Patel, S.B., Becker, J.W., Wang, Q., Desponts, C., Waddleton, D., Skorey, K., Cromlish, W., Bayly, C., Therien, M., Gauthier, J.Y., Li, C.S., Lau, C.K., Ramachandran, C., Kennedy, B.P., Asante-Appiah, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.215 

Literature

The Structural Basis for the Selectivity of Benzotriazole Inhibitors of Ptp1B

Scapin, G., Patel, S.B., Becker, J.W., Wang, Q., Desponts, C., Waddleton, D., Skorey, K., Cromlish, W., Bayly, C., Therien, M., Gauthier, J.Y., Li, C.S., Lau, C.K., Ramachandran, C., Kennedy, B.P., Asante-Appiah, E.

(2003) Biochemistry 42: 11451-11459

• PubMed: 14516196 
• DOI: 10.1021/bi035098j
• Primary Citation of Related Structures:  
  1Q6M, 1Q6J, 1Q6T, 1Q6S, 1Q6P, 1Q6N


• PubMed Abstract: 
  

Protein tyrosine phosphatase 1B (PTP1B) has been implicated in the regulation of the insulin signaling pathway and represents an attractive target for the design of inhibitors in the treatment of type 2 diabetes and obesity. Inspection of the structure of PTP1B indicates that potent PTP1B inhibitors may be obtained by targeting a secondary aryl phosphate-binding site as well as the catalytic site. We report here the crystal structures of PTP1B in complex with first and second generation aryldifluoromethyl-phosphonic acid inhibitors. While all compounds bind in a previously unexploited binding pocket near the primary binding site, the second generation compounds also reach into the secondary binding site, and exhibit moderate selectivity for PTP1B over the closely related T-cell phosphatase. The molecular basis for the selectivity has been confirmed by single point mutation at position 52, where the two phosphatases differ by a phenylalanine-to-tyrosine switch. These compounds present a novel platform for the development of potent and selective PTP1B inhibitors.

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Organizational Affiliation: 

Merck Research Laboratory, P. O. Box 2000, Rahway, New Jersey 07065, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine phosphatase, non-receptor type 1	A	310	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1 OR PTP1B, 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
335	A	[4-(2-(1H-1,2,3-BENZOTRIAZOL-1-YL)-3-{4-[DIFLUORO(PHOSPHONO)METHYL]PHENYL}-2-PHENYLPROPYL)PHENYL](DIFLUORO)METHYLPHOSPHONIC ACID C29 H25 F4 N3 O6 P2 WNNXXNZHCLRWMD-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
335	IC50 :  16   nM  PDBBind
335	IC50:  16   nM  BindingDB
335	IC50:  120   nM  BindingDB
335	IC50:  16   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.215 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.838	α = 90
b = 86.838	β = 90
c = 139.693	γ = 90

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
CNX	refinement
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-13 
• Released Date: 2003-09-30 
Deposition Author(s): Scapin, G., Patel, S.B., Becker, J.W., Wang, Q., Desponts, C., Waddleton, D., Skorey, K., Cromlish, W., Bayly, C., Therien, M., Gauthier, J.Y., Li, C.S., Lau, C.K., Ramachandran, C., Kennedy, B.P., Asante-Appiah, E.

Revision History 

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description