2ZMM | pdb_00002zmm

Crystal structure of PTP1B-inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2ZMM/pdb

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


• Deposited: 2008-04-19 Released: 2008-10-07 
• Deposition Author(s): Xu, W., Wu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.213 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure-based optimization of protein tyrosine phosphatase-1 B inhibitors: capturing interactions with arginine 24

Wan, Z.-K., Lee, J., Hotchandani, R., Moretto, A., Binnun, E., Wilson, D.P., Kirincich, S.J., Follows, B.C., Ipek, M., Xu, W., Joseph-McCarthy, D., Zhang, Y.-L., Tam, M., Erbe, D.V., Tobin, J.F., Li, W., Tam, S.Y., Mansour, T.S., Wu, J.

(2008) ChemMedChem 3: 1525-1529

• PubMed: 18798205 
• DOI: https://doi.org/10.1002/cmdc.200800188
• Primary Citation Related Structures: 
  2ZMM, 2ZN7

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Organizational Affiliation: 
• Chemical and Screening Sciences, Wyeth Research, 200 Cambridgepark Drive, Cambridge, MA 02140, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.58 kDa 
• Atom Count: 2,757 
• Modeled Residue Count: 297 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	299	Homo sapiens	Mutation(s): 0  Gene Names: PTP1B 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
35B	I [auth A]	4-bromo-3-(carboxymethoxy)-5-{3-[cyclohexyl(methylcarbamoyl)amino]phenyl}thiophene-2-carboxylic acid C21 H23 Br N2 O6 S PXYOQUGPJYIRGZ-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.213 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.02	α = 90
b = 88.02	β = 90
c = 103.676	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Xu, W., Wu, J.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description