2HB1

Crystal Structure of PTP1B with Monocyclic Thiophene Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2HB1/pdb

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


• Deposited: 2006-06-13 Released: 2006-08-29 
• Deposition Author(s): Xu, W., Wan, Z.-K., Lee, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

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 of 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: 35.11 kDa 
• Atom Count: 2,611 
• Modelled 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
512	B [auth A]	4-BROMO-3-(CARBOXYMETHOXY)THIOPHENE-2-CARBOXYLIC ACID C7 H5 Br O5 S VDPVVSMGWNMCBP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
512	BindingDB:  2HB1	Ki: 1.60e+5 (nM) from 1 assay(s)
	PDBBind:  2HB1	Ki: 1.60e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.538	α = 90
b = 88.538	β = 90
c = 104.202	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations