2CNE

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

• PDB DOI: https://doi.org/10.2210/pdb2CNE/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: 0.237 
• R-Value Work: 0.197 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36.72 kDa 
• Atom Count: 2,665 
• Modelled Residue Count: 287 
• Deposited Residue Count: 304 
• Unique protein chains: 1

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  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 GTEx:  ENSG00000196396

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DFJ	B [auth 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
BOG	E [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
DFJ	BindingDB:  2CNE	Ki: 1.7 (nM) from 1 assay(s)
		IC50: 1.7 (nM) from 1 assay(s)
	Binding MOAD:  2CNE	IC50: 1.7 (nM) from 1 assay(s)
	PDBBind:  2CNE	IC50: 1.7 (nM) from 1 assay(s)

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 = 62.11	α = 90
b = 70.98	β = 90
c = 83.78	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary