2FJM | pdb_00002fjm

The structure of phosphotyrosine phosphatase 1B in complex with compound 2

• PDB DOI: https://doi.org/10.2210/pdb2FJM/pdb

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


• Deposited: 2006-01-03 Released: 2006-01-17 
• Deposition Author(s): Asante-Appiah, E., Patel, S., Desponts, C., Taylor, J.M., Lau, C., Dufresne, C., Therien, M., Friesen, R., Becker, J.W., Leblanc, Y., Scapin, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Conformation-assisted inhibition of protein-tyrosine phosphatase-1B elicits inhibitor selectivity over T-cell protein-tyrosine phosphatase.

Asante-Appiah, E., Patel, S., Desponts, C., Taylor, J.M., Lau, C., Dufresne, C., Therien, M., Friesen, R., Becker, J.W., Leblanc, Y., Kennedy, B.P., Scapin, G.

(2006) J Biological Chem 281: 8010-8015

• PubMed: 16407290 
• DOI: https://doi.org/10.1074/jbc.M511827200
• Primary Citation Related Structures: 
  2FJM, 2FJN


• PubMed Abstract: 
  

  PTP-1B represents an attractive target for the treatment of type 2 diabetes and obesity. Given the role that protein phosphatases play in the regulation of many biologically relevant processes, inhibitors against PTP-1B must be not only potent, but also selective. It has been extremely difficult to synthesize inhibitors that are selective over the highly homologous TCPTP. We have successfully exploited the conservative Leu119 to Val substitution between the two enzymes to synthesize a PTP-1B inhibitor that is an order of magnitude more selective over TCPTP. Structural analyses of PTP-1B/inhibitor complexes show a conformation-assisted inhibition mechanism as the basis for selectivity. Such an inhibitory mechanism may be applicable to other homologous enzymes.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Merck Frosst Center for Therapeutic Research, Pointe-Claire, Dorval, Quebec H9R 4P8, Canada. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.75 kDa 
• Atom Count: 5,126 
• Modeled Residue Count: 570 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase, non-receptor type 1	A, B	310	Homo sapiens	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
073	D [auth A], G [auth B]	(4-{(2S,4E)-2-(1H-1,2,3-BENZOTRIAZOL-1-YL)-2-[4-(METHOXYCARBONYL)PHENYL]-5-PHENYLPENT-4-ENYL}PHENYL)(DIFLUORO)METHYLPHOSPHONIC ACID C32 H28 F2 N3 O5 P GWWTUJWRRCTCSI-AOCUTKQBSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
073	BindingDB:  2FJM	IC50: min: 29, max: 142 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.431	α = 90
b = 86.621	β = 90
c = 139.193	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): Asante-Appiah, E., Patel, S., Desponts, C., Taylor, J.M., Lau, C., Dufresne, C., Therien, M., Friesen, R., Becker, J.W., Leblanc, Y., Scapin, G.

Revision History  

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.6: 2023-08-30
  Changes: Data collection, Refinement description