2QBP

Crystal structure of ptp1b-inhibitor complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Structure-based optimization of protein tyrosine phosphatase 1B inhibitors: from the active site to the second phosphotyrosine binding site.

Wilson, D.P., Wan, Z.K., Xu, W.X., Kirincich, S.J., Follows, B.C., Joseph-McCarthy, D., Foreman, K., Moretto, A., Wu, J., Zhu, M., Binnun, E., Zhang, Y.L., Tam, M., Erbe, D.V., Tobin, J., Xu, X., Leung, L., Shilling, A., Tam, S.Y., Mansour, T.S., Lee, J.

(2007) J Med Chem 50: 4681-4698

  • DOI: https://doi.org/10.1021/jm0702478
  • Primary Citation of Related Structures:  
    2QBP, 2QBQ, 2QBR, 2QBS

  • PubMed Abstract: 

    • Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin receptor pathways and thus an attractive therapeutic target for diabetes and obesity. Starting with a high micromolar lead compound, structure-based optimization of novel PTP1B inhibitors by extension of the molecule from the enzyme active site into the second phosphotyrosine binding site is described ...

    Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin receptor pathways and thus an attractive therapeutic target for diabetes and obesity. Starting with a high micromolar lead compound, structure-based optimization of novel PTP1B inhibitors by extension of the molecule from the enzyme active site into the second phosphotyrosine binding site is described. Medicinal chemistry, guided by X-ray complex structure and molecular modeling, has yielded low nanomolar PTP1B inhibitors in an efficient manner. Compounds from this chemical series were found to be actively transported into hepatocytes. This active uptake into target tissues could be one of the possible avenues to overcome the poor membrane permeability of PTP1B inhibitors.

    Related Citations: 
    • Bicyclic and Tricyclic Thiophenes as Protein Tyrosine Phosphatase 1B Inhibitor
      Moretto, A.F., Kirincich, S.J., Xu, W.X., Smith, M.J., Wan, Z.-K., Wilson, D.P., Follows, B.C., Binnun, E., Joseph-Mccarthy, D., Foreman, K., Erbe, D.V., Zhang, Y.-L., Tam, S.K., Tam, S.Y., Lee, J.
      (2006) Bioorg Med Chem 14: 2162
    Organizational Affiliation: 

    Chemical and Screening Sciences, and Cardiovascular and Metabolic Diseases, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1299Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
527
Query on 527
Download Ideal Coordinates CCD File 
B [auth A]5-(3-{[1-(BENZYLSULFONYL)PIPERIDIN-4-YL]AMINO}PHENYL)-4-BROMO-3-(CARBOXYMETHOXY)THIOPHENE-2-CARBOXYLIC ACID
C25 H25 Br N2 O7 S2
FEPAAIQAIYOLJA-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
527 Binding MOAD:  2QBP Ki: 4 (nM) from 1 assay(s)
PDBBind:  2QBP Ki: 4 (nM) from 1 assay(s)
BindingDB:  2QBP Ki: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.456α = 90
b = 88.456β = 90
c = 104.29γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2008-03-18 
    • Deposition Author(s): Xu, W.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description