Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 36421.28 
• Atom Count: 2399 
• Residue Count: 304 
• Unique protein chains: 1

2CMC

Structural Basis for Inhibition of Protein Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics

• DOI: 10.2210/pdb2CMC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-05-04 Released: 2006-08-17 
• Deposition Author(s): Ala, P.J., Gonneville, L., Hillman, M.C., Becker-Pasha, M., Wei, M., Reid, B.G., Klabe, R., Yue, E.W., Wayland, B., Douty, B., Combs, A.P., Polam, P., Wasserman, Z., Bower, M., Burn, T.C., Hollis, G.F., Wynn, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.263 
• R-Value Work: 0.209 

Literature

Structural Basis for Inhibition of Protein-Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics.

Ala, P.J., Gonneville, L., Hillman, M.C., Becker-Pasha, M., Wei, M., Reid, B.G., Klabe, R., Yue, E.W., Wayland, B., Douty, B., Polam, P., Wasserman, Z., Bower, M., Combs, A.P., Burn, T.C., Hollis, G.F., Wynn, R.

(2006) J.Biol.Chem. 281: 32784

• PubMed: 16916797 
• DOI: 10.1074/jbc.M606873200
• Primary Citation of Related Structures:  
  2CMB, 2CMA, 2CM8, 2CM7, 2CM3, 2CM2


• PubMed Abstract: 
  

Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe(182) of the flap, and the side chain of Arg(221). When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors.

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Organizational Affiliation: 

Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1	A	304	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1 (PTP1B) EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens) Go to Gene View: PTPN1 Go to UniProtKB:  P18031

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DFM	A	N-ACETYL-L-PHENYLALANYL-4-[DIFLUORO(PHOSPHONO)METHYL]-L-PHENYLALANINAMIDE DIFLUOROMETHYLPHOSPHONIC ACID ANALOG C21 H24 F2 N3 O6 P KPMMESISHWWXNM-ROUUACIJSA-N
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DFM	IC50: 1700 - 1750 nM (100) BINDINGDB
DFM	IC50: 1750 nM BINDINGMOAD
DFM	IC50: 1750 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.263 
• R-Value Work: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.200	α = 90.00
b = 70.900	β = 90.00
c = 83.310	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-04 
• Released Date: 2006-08-17 
• Deposition Author(s): Ala, P.J., Gonneville, L., Hillman, M.C., Becker-Pasha, M., Wei, M., Reid, B.G., Klabe, R., Yue, E.W., Wayland, B., Douty, B., Combs, A.P., Polam, P., Wasserman, Z., Bower, M., Burn, T.C., Hollis, G.F., Wynn, R.

Revision History 

• Version 1.0: 2006-08-17
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-07-05
  Type: Data collection