1WAX | pdb_00001wax

Protein tyrosine phosphatase 1B with active site inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1WAX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-10-28 Released: 2005-01-27 
• Deposition Author(s): Hartshorn, M.J., Murray, C.W., Cleasby, A., Frederickson, M., Tickle, I.J., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Fragment-Based Lead Discovery Using X-Ray Crystallography

Hartshorn, M.J., Murray, C.W., Cleasby, A., Frederickson, M., Tickle, I.J., Jhoti, H.

(2005) J Med Chem 48: 403

• PubMed: 15658854 
• DOI: https://doi.org/10.1021/jm0495778
• Primary Citation Related Structures: 
  1W7H, 1WAX, 1WAY, 1WBG, 1WBO, 1WBU, 1WCC


• PubMed Abstract: 
  

  Fragment screening offers an alternative to traditional screening for discovering new leads in drug discovery programs. This paper describes a fragment screening methodology based on high throughput X-ray crystallography. The method is illustrated against five proteins (p38 MAP kinase, CDK2, thrombin, ribonuclease A, and PTP1B). The fragments identified have weak potency (>100 microM) but are efficient binders relative to their size and may therefore represent suitable starting points for evolution to good quality lead compounds. The examples illustrate that a range of molecular interactions (i.e., lipophilic, charge-charge, neutral hydrogen bonds) can drive fragment binding and also that fragments can induce protein movement. We believe that the method has great potential for the discovery of novel lead compounds against a range of targets, and the companion paper illustrates how lead compounds have been identified for p38 MAP kinase starting from fragments such as those described in this paper.

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Organizational Affiliation: 
• Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 37.58 kDa 
• Atom Count: 2,677 
• Modeled Residue Count: 298 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN-TYROSINE PHOSPHATASE	A	321	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000196396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LO1	C [auth A]	[[4-(AMINOMETHYL)PHENYL]AMINO]OXO-ACETIC ACID, C9 H10 N2 O3 RKILOCCSAVHHJT-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.095	α = 90
b = 88.095	β = 90
c = 104.497	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
IN-HOUSE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-27 
Deposition Author(s): Hartshorn, M.J., Murray, C.W., Cleasby, A., Frederickson, M., Tickle, I.J., Jhoti, H.

Revision History  

• Version 1.0: 2005-01-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description