2VEV

CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B IN COMPLEX WITH AN ISOTHIAZOLIDINONE-CONTAINING INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb2VEV/pdb

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


• Deposited: 2007-10-27 Released: 2007-11-06 
• Deposition Author(s): Douty, B., Wayland, B., Ala, P.J., Bower, M.J., Pruitt, J., Bostrom, L., Wei, M., Klabe, R., Gonneville, L., Wynn, R., Burn, T.C., Liu, P.C.C., Combs, A.P., Yue, E.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

Isothiazolidinone Inhibitors of Ptp1B Containing Imidazoles and Imidazolines

Douty, B., Wayland, B., Ala, P.J., Bower, M.J., Pruitt, J., Bostrom, L., Wei, M., Klabe, R., Gonneville, L., Wynn, R., Burn, T.C., Liu, P.C.C., Combs, A.P., Yue, E.W.

(2008) Bioorg Med Chem Lett 18: 66

• PubMed: 18037290 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.012
• Primary Citation of Related Structures:  
  2VEU, 2VEV, 2VEW, 2VEX, 2VEY


• PubMed Abstract: 
  

  The structure-based design and synthesis of isothiazolidinone (IZD) inhibitors of PTP1B containing imidazoles and imidazolines and their modification to interact with the B site of PTP1B are described here. The X-ray crystal structures of 3I and 4I complexed with PTP1B were solved and revealed the inhibitors are interacting extensively with the B site of the enzyme.

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Organizational Affiliation: 

Incyte Corporation, Discovery Chemistry, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 38.01 kDa 
• Atom Count: 2,843 
• Modelled Residue Count: 299 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IZ2	B [auth A]	N-[(1S)-1-(4-benzyl-1H-imidazol-2-yl)-2-{4-[(5S)-1,1-dioxido-3-oxoisothiazolidin-5-yl]phenyl}ethyl]-3-(trifluoromethyl)benzenesulfonamide C28 H25 F3 N4 O5 S2 UMIIBUJRMKQTQV-DQEYMECFSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IZ2	PDBBind:  2VEV	IC50: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.95	α = 90
b = 73.02	β = 90
c = 88.29	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Douty, B., Wayland, B., Ala, P.J., Bower, M.J., Pruitt, J., Bostrom, L., Wei, M., Klabe, R., Gonneville, L., Wynn, R., Burn, T.C., Liu, P.C.C., Combs, A.P., Yue, E.W.

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2020-11-18
  Changes: Derived calculations, Other, Structure summary
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references