1ECV

CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH 5-IODO-2-(OXALYL-AMINO)-BENZOIC ACID

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

2-(oxalylamino)-benzoic acid is a general, competitive inhibitor of protein-tyrosine phosphatases.

Andersen, H.S., Iversen, L.F., Jeppesen, C.B., Branner, S., Norris, K., Rasmussen, H.B., Moller, K.B., Moller, N.P.

(2000) J.Biol.Chem. 275: 7101-7108

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Protein-tyrosine phosphatases (PTPs) are critically involved in regulation of signal transduction processes. Members of this class of enzymes are considered attractive therapeutic targets in several disease states, e.g. diabetes, cancer, and inflamma ...

    Protein-tyrosine phosphatases (PTPs) are critically involved in regulation of signal transduction processes. Members of this class of enzymes are considered attractive therapeutic targets in several disease states, e.g. diabetes, cancer, and inflammation. However, most reported PTP inhibitors have been phosphorus-containing compounds, tight binding inhibitors, and/or inhibitors that covalently modify the enzymes. We therefore embarked on identifying a general, reversible, competitive PTP inhibitor that could be used as a common scaffold for lead optimization for specific PTPs. We here report the identification of 2-(oxalylamino)-benzoic acid (OBA) as a classical competitive inhibitor of several PTPs. X-ray crystallography of PTP1B complexed with OBA and related non-phosphate low molecular weight derivatives reveals that the binding mode of these molecules to a large extent mimics that of the natural substrate including hydrogen bonding to the PTP signature motif. In addition, binding of OBA to the active site of PTP1B creates a unique arrangement involving Asp(181), Lys(120), and Tyr(46). PTP inhibitors are essential tools in elucidating the biological function of specific PTPs and they may eventually be developed into selective drug candidates. The unique enzyme kinetic features and the low molecular weight of OBA makes it an ideal starting point for further optimization.

    Organizational Affiliation: 

    MedChem Research I, Novo Nordisk, DK-2880 Bagsvaerd, Denmark. hsa@novo.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN-TYROSINE PHOSPHATASE 1B
A
298Homo sapiensMutation(s): 0 
Gene Names: PTPN1 (PTP1B)
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Go to Gene View: PTPN1
Go to UniProtKB:  P18031
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
878
Query on 878
Download SDF File 
Download CCD File 
A
5-IODO-2-(OXALYL-AMINO)-BENZOIC ACID
NOVO NORDISK A/S COMPOUND
C9 H6 I N O5
SHSWHSQPJKMCPN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
878Ki: 14000 - 14125.4 nM (99) BINDINGDB
878Ki: 14000 nM BINDINGMOAD
878Ki: 14000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.870α = 90.00
b = 87.870β = 90.00
c = 103.120γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection