2CNE

Structural Insights into the Design of Nonpeptidic Isothiazolidinone- Containing Inhibitors of Protein Tyrosine Phosphatase 1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Insights Into the Design of Nonpeptidic Isothiazolidinone-Containing Inhibitors of Protein- Tyrosine Phosphatase 1B.

Ala, P.J.Gonneville, L.Hillman, M.Becker-Pasha, M.Yue, E.W.Douty, B.Wayland, B.Polam, P.Crawley, M.L.Mclaughlin, E.Sparks, R.B.Glass, B.Takvorian, A.Combs, A.P.Burn, T.C.Hollis, G.F.Wynn, R.

(2006) J Biol Chem 281: 38013

  • DOI: 10.1074/jbc.M607913200
  • Primary Citation of Related Structures:  
    2CNI, 2CNH, 2CNG, 2CNF, 2CNE

  • PubMed Abstract: 
  • Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability we ...

    Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability were simultaneously improved by replacing the polar peptidic backbone of the inhibitor with nonpeptidic moieties. The C-terminal primary amide was replaced with a benzimidazole ring, which hydrogen bonds to the carboxylate of Asp(48), and the N terminus of the peptide was replaced with an aryl sulfonamide, which hydrogen bonds to Asp(48) and the backbone NH of Arg(47) via a water molecule. Although both substituents retain the favorable hydrogen bonding network of the peptide scaffold, their aryl rings interact weakly with the protein. The aryl ring of benzimidazole is partially solvent exposed and only participates in van der Waals interactions with Phe(182) of the flap. The aryl ring of aryl sulfonamide adopts an unexpected conformation and only participates in intramolecular pi-stacking interactions with the benzimidazole ring. These results explain the flat SAR for substitutions on both rings and the reason why unsubstituted moieties were selected as candidates. Finally, substituents ortho to the IZD heterocycle on the aryl ring of the IZD-phenyl moiety bind in a small narrow site adjacent to the primary phosphate binding pocket. The crystal structure of an o-chloro derivative reveals that chlorine interacts extensively with residues in the small site. The structural insights that have led to the discovery of potent benzimidazole aryl sulfonamide o-substituted derivatives are discussed in detail.


    Organizational Affiliation

    Incyte Corporation, Wilmington, Delaware 19880, USA. pauljala@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1A304Homo sapiensMutation(s): 0 
Gene Names: PTPN1PTP1B
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS  P18031
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DFJ
Query on DFJ

Download CCD File 
A
N-({4-[DIFLUORO(PHOSPHONO)METHYL]PHENYL}ACETYL)-L-PHENYLALANYL-4-[DIFLUORO(PHOSPHONO)METHYL]-L-PHENYLALANINAMIDE
C28 H29 F4 N3 O9 P2
LGZYIQKUXWAUAL-GOTSBHOMSA-N
 Ligand Interaction
BOG
Query on BOG

Download CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DFJIC50 :  1.7000000476837158   nM  PDBBind
DFJIC50:  1.7000000476837158   nM  Binding MOAD
DFJKi:  1.7000000476837158   nM  BindingDB
DFJIC50:  1.7000000476837158   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.11α = 90
b = 70.98β = 90
c = 83.78γ = 90
Software Package:
Software NamePurpose
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-27
    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: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary