1C85

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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

  • DOI: 10.1074/jbc.275.10.7101
  • Structures With Same Primary Citation

  • 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 (PROTEIN-TYROSINE PHOSPHATASE 1B)
A
298Homo sapiensMutation(s): 0 
Gene Names: PTPN1PTP1B
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS  P18031
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OBA
Query on OBA

Download CCD File 
A
2-(OXALYL-AMINO)-BENZOIC ACID
C9 H7 N O5
QBYNNSFEMMNINN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OBAKi :  23000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.87α = 90
b = 87.87β = 90
c = 103.12γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection