1ECV | pdb_00001ecv
CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH 5-IODO-2-(OXALYL-AMINO)-BENZOIC ACID
- PDB DOI: https://doi.org/10.2210/pdb1ECV/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2000-01-26 Released: 2000-03-15
- Deposition Author(s): Andersen, H.S., Iversen, L.F., Branner, S., Rasmussen, H.B., Moller, N.P.H.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.249 (Depositor)
- R-Value Work: 0.194 (Depositor)
wwPDB Validation 3D Report Full Report
- 👁 Image
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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 Biological Chem 275: 7101-7108
- PubMed: 10702277 Search on PubMed
- DOI: https://doi.org/10.1074/jbc.275.10.7101
- Primary Citation Related Structures:
1C83, 1C84, 1C85, 1ECV - 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 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.
- MedChem Research I, Novo Nordisk, DK-2880 Bagsvaerd, Denmark. hsa@novo.dk
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (878)
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (878)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 35.23 kDa
- Atom Count: 2,696
- Modeled Residue Count: 297
- Deposited Residue Count: 298
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PROTEIN-TYROSINE PHOSPHATASE 1B | 298 | Homo sapiens | Mutation(s): 0 EC: 3.1.3.48 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P18031 (Homo sapiens) Explore P18031 Go to UniProtKB: P18031 | |||||
PHAROS: P18031 GTEx: ENSG00000196396 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P18031 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 878 Query on 878 Download Ideal Coordinates CCD File | E [auth A] | 5-IODO-2-(OXALYL-AMINO)-BENZOIC ACID C9 H6 I N O5 SHSWHSQPJKMCPN-UHFFFAOYSA-N | 👁 Image | ||
| ACT Query on ACT Download Ideal Coordinates CCD File | B [auth A], C [auth A], D [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | 👁 Image | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.249 (Depositor)
- R-Value Work: 0.194 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.87 | α = 90 |
| b = 87.87 | β = 90 |
| c = 103.12 | γ = 120 |
| Software Name | Purpose |
|---|---|
| AMoRE | phasing |
| X-PLOR | refinement |
| DENZO | data reduction |
| CCP4 | data scaling |
Deposition Data
- Released Date: 2000-03-15 Deposition Author(s): Andersen, H.S., Iversen, L.F., Branner, S., Rasmussen, H.B., Moller, N.P.H.
Revision History (Full details and data files)
- Version 1.0: 2000-03-15
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2018-03-07
Changes: Data collection - Version 1.4: 2024-02-07
Changes: Data collection, Database references, Derived calculations
