1Q1M

A Highly Efficient Approach to a Selective and Cell Active PTP1B inhibitors

PDB DOI: https://doi.org/10.2210/pdb1Q1M/pdb

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

Deposited: 2003-07-22 Released: 2003-09-16
Deposition Author(s): Liu, G., Xin, Z., Pei, Z., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Zhao, H., Lubben, T.H., Ballaron, S.J., Haasch, D.L., Kaszubska, W., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.223
R-Value Work: 0.187
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor.

Liu, G., Xin, Z., Pei, Z., Hajduk, P.J., Abad-Zapatero, C., Hutchins, C.W., Zhao, H., Lubben, T.H., Ballaron, S.J., Haasch, D.L., Kaszubska, W., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.

(2003) J Med Chem 46: 4232-4235

PubMed: 13678400 Search on PubMed
DOI: https://doi.org/10.1021/jm034122o
Primary Citation of Related Structures:
1Q1M

PubMed Abstract:

Using an NMR-based fragment screening and X-ray crystal structure-based assembly, starting with millimolar ligands for both the catalytic site and the second phosphotyrosine binding site, we have identified a small-molecule inhibitor of protein tyrosine phosphatase 1B with low micromolar inhibition constant, high selectivity (30-fold) over the highly homologous T-cell protein tyrosine phosphatase, and good cellular activity in COS-7 cells.

Related Citations:

Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy.
Szczepankiewicz, B.G., Liu, G., Hajduk, P.J., Abad-Zapatero, C., Pei, Z., Xin, Z., Lubben, T.H., Trevillyan, J.M., Stashko, M.A., Ballaron, S.J., Liang, H., Huang, F., Hutchins, C.W., Fesik, S.W., Jirousek, M.R.
(2003) J Am Chem Soc 125: 4087

Potent, Selective Inhibitors of Protein Tyrosine Phosphatase 1B
Xin, Z., Oost, T.K., Abad-Zapatero, C., Hajduk, P.J., Pei, Z., Szczepankiewicz, B.G., Hutchins, C.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Trevillyan, J.M., Jirousek, M.R., Liu, G.
(2003) Bioorg Med Chem Lett 13: 1887

Discovery and Structure-Activity Relationship of Oxalylarylaminobenzoic Acids as Inhibitors of Protein Tyrosine Phosphatase 1B
Liu, G., Szczepankiewicz, B.G., Pei, Z., Janowich, D.A., Xin, Z., Hadjuk, P.J., Abad-Zapatero, C., Liang, H., Hutchins, C.W., Fesik, S.W., Ballaron, S.J., Stashko, M.A., Lubben, T., Mika, A.K., Zinker, B.A., Trevillyan, J.M., Jirousek, M.R.
(2003) J Med Chem 46: 2093

Selective Protein Tyrosine Phosphatase 1B Inhibitors: Targeting the Second Phosphotyrosine Binding Site with Non-Carboxylic Acid-Containing Ligands
Liu, G., Xin, Z., Liang, H., Abad-Zapatero, C., Hajduk, P.J., Janowick, D.A., Szczepankiewicz, B.G., Pei, Z., Hutchins, C.W., Ballaron, S.J., Stashko, M.A., Lubben, T.H., Berg, C.E., Rondinone, C.M., Trevillyan, J.M., Jirousek, M.R.
() To be published --: --

Discovery and SAR of Novel, Potent and Selective Protein Tyrosine Phosphatase 1B Inhibitors
Pei, Z., Li, X., Liu, G., Abad-Zapatero, C., Lubben, T., Zhang, T., Ballaron, S.J., Hutchins, C.W., Trevillyan, J.M., Jirousek, M.R.
() To be published --: --

Organizational Affiliation:

Metabolic Disease Research and Advanced Technology, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-6098, USA. gaang.liu@abbott.com

Macromolecule Content

Total Structure Weight: 37.78 kDa
Atom Count: 2,589
Modelled Residue Count: 299
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine phosphatase, non-receptor type 1	A	321	Homo sapiens	Mutation(s): 0 Gene Names: PTPN1 OR PTP1B, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18031
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
234 Query on 234 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-{2-FLUORO-5-[3-(3-HYDROXY-2-METHOXYCARBONYL-PHENOXY)-PROPENYL]-PHENYL}-ISOXAZOLE-3-CARBOXYLIC ACID C₂₁ H₁₆ F N O₇ QKHWJUMLYAYZFS-ONEGZZNKSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
234	BindingDB: 1Q1M	Ki: min: 6310, max: 7000 (nM) from 4 assay(s)
	BindingDB: 1Q1M	IC50: min: 6900, max: 1.10e+5 (nM) from 2 assay(s)
	PDBBind: 1Q1M	Ki: 6900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.223
R-Value Work: 0.187
R-Value Observed: 0.208
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.294	α = 90
b = 88.294	β = 90
c = 104.378	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MAR345	data collection
HKL-2000	data scaling
CNX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-09-16
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
Version 1.4: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description