7UW6 | pdb_00007uw6

The co-crystal structure of low molecular weight protein tyrosine phosphatase (LMW-PTP) with a small molecule inhibitor SPAA-2

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

  • Deposited: 2022-05-02 Released: 2022-10-19 
  • Deposition Author(s): Wang, J., Zhang, Z.Y.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of Active-Site-Directed, Highly Potent, Selective, and Orally Bioavailable Low-Molecular-Weight Protein Tyrosine Phosphatase Inhibitors.

He, R.Wang, J.Yu, Z.H.Moyers, J.S.Michael, M.D.Durham, T.B.Cramer, J.W.Qian, Y.Lin, A.Wu, L.Noinaj, N.Barrett, D.G.Zhang, Z.Y.

(2022) J Med Chem 65: 13892-13909

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01143
  • Primary Citation Related Structures: 
    7UW6

  • PubMed Abstract: 

    Protein tyrosine phosphatases constitute an important class of drug targets whose potential has been limited by the paucity of drug-like small-molecule inhibitors. We recently described a class of active-site-directed, moderately selective, and potent inhibitors of the low-molecular-weight protein tyrosine phosphatase (LMW-PTP). Here, we report our extensive structure-based design and optimization effort that afforded inhibitors with vastly improved potency and specificity. The leading compound inhibits LMW-PTP potently and selectively ( K i = 1.2 nM, >8000-fold selectivity). Many compounds exhibit favorable drug-like properties, such as low molecular weight, weak cytochrome P450 inhibition, high metabolic stability, moderate to high cell permeability (Papp > 0.2 nm/s), and moderate to good oral bioavailability (% F from 23 to 50% in mice), and therefore can be used as in vivo chemical probes to further dissect the complex biological as well as pathophysiological roles of LMW-PTP and for the development of therapeutics targeting LMW-PTP.


  • Organizational Affiliation
    • Lilly Research Laboratories, Eli Lilly and Company, 307 E Merrill Street, Indianapolis, Indiana 46225, United States.

Macromolecule Content 

  • Total Structure Weight: 20.38 kDa 
  • Atom Count: 1,527 
  • Modeled Residue Count: 154 
  • Deposited Residue Count: 177 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Low molecular weight phosphotyrosine protein phosphatase177Homo sapiensMutation(s): 0 
Gene Names: ACP1
EC: 3.1.3.48 (PDB Primary Data), 3.1.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24666 (Homo sapiens)
Explore P24666 
Go to UniProtKB:  P24666
PHAROS:  P24666
GTEx:  ENSG00000143727 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24666
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OIF
(Subject of Investigation/LOI)

Query on OIF



Download:Ideal Coordinates CCD File
B [auth A]2-[(1,3-benzothiazol-2-yl)amino]-2-oxoethane-1-sulfonic acid
C9 H8 N2 O4 S2
SYEABNIGTPGICH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.873α = 90
b = 54.566β = 90
c = 95.242γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA207288
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesRO1 069202

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description