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: 36.42 kDa 
• Atom Count: 2577 
• Modelled Residue Count: 286 
• Deposited 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)
• Mutation(s): No 


• 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: 2.20 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:  
  2CM3, 2CM2, 2CM8, 2CM7, 2CMC, 2CMB, 2CMA


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P18031  Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS:  P18031 GTEx:  ENSG00000196396

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DFM	IC50:  1750   nM  Binding MOAD
DFM	IC50:  1749847   nM  BindingDB
DFM	IC50 :  1750   nM  PDBBind
DFM	IC50:  1700   nM  BindingDB
DFM	IC50:  1750   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.2	α = 90
b = 70.9	β = 90
c = 83.31	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: 2006-05-04 
• 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
  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