Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37.99 kDa 
• Atom Count: 2736 
• Residue Count: 297 
• Unique protein chains: 1

2CNH

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

• DOI: 10.2210/pdb2CNH/pdb

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


• Deposited: 2006-05-21 Released: 2006-09-27 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 

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

• PubMed: 17028182 
• 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 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.

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Organizational Affiliation: 

Incyte Corporation, Wilmington, Delaware 19880, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1	A	321	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1, PTP1B EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS  P18031 GTEx  ENSG00000196396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IZB	A	N-[(1S)-1-(1H-BENZIMIDAZOL-2-YL)-2-{4-[(5S)-1,1-DIOXIDO-3-OXOISOTHIAZOLIDIN-5-YL]PHENYL}ETHYL]-4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZINE-7-SULFONAMIDE C27 H27 N5 O6 S2 QNAGNPUNGCBSIJ-DHLKQENFSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IZB	IC50:  59   nM  Binding MOAD
IZB	IC50:  59   nM  BindingDB
IZB	IC50 :  59   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.9	α = 90
b = 71.41	β = 90
c = 87.58	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-21 
• Released Date: 2006-09-27 
Deposition Author(s): 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.

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