2H4K | pdb_00002h4k

Crystal structure of PTP1B with a monocyclic thiophene inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2H4K/pdb

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


• Deposited: 2006-05-24 Released: 2006-08-29 
• Deposition Author(s): Xu, W., Wan, Z.-K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.260 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Monocyclic thiophenes as protein tyrosine phosphatase 1B inhibitors: Capturing interactions with Asp48.

Wan, Z.K., Lee, J., Xu, W., Erbe, D.V., Joseph-McCarthy, D., Follows, B.C., Zhang, Y.L.

(2006) Bioorg Med Chem Lett 16: 4941-4945

• PubMed: 16806920 
• DOI: https://doi.org/10.1016/j.bmcl.2006.06.051
• Primary Citation Related Structures: 
  2H4G, 2H4K, 2HB1


• PubMed Abstract: 
  

  A series of monocyclic thiophenes was designed and synthesized as PTP1B inhibitors. Guided by X-ray co-crystal structural information and computational modeling, rational design led to key interactions with Asp48 and improved inhibitory potency against PTP1B.

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Organizational Affiliation: 
• Chemical and Screening Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.19 kDa 
• Atom Count: 2,558 
• Modeled Residue Count: 297 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	299	Homo sapiens	Mutation(s): 0  Gene Names: 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 GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
509	B [auth A]	4-BROMO-3-(CARBOXYMETHOXY)-5-PHENYLTHIOPHENE-2-CARBOXYLIC ACID C13 H9 Br O5 S MVDWLRCTJUXCCB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.260 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.996	α = 90
b = 87.996	β = 90
c = 103.722	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Xu, W., Wan, Z.-K.

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations