Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37899.21 
• Atom Count: 2340 
• Residue Count: 321 
• Unique protein chains: 1

1NL9

Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Compound 12 Using a Linked-Fragment Strategy

• DOI: 10.2210/pdb1NL9/pdb

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


• Deposited: 2003-01-06 Released: 2003-04-08 
• Deposition Author(s): Szczepankiewicz, B.G., Liu, G., Hajduk, P.J., Abad-Zapatero, C., Pei, Z., Xin, Z., Lubben, T., Trevillyan, J.M., Stashko, M.A., Ballaron, S.J., Liang, H., Huang, F., Hutchins, C.W., Fesik, S.W., Jirousek, M.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.247 
• R-Value Work: 0.192 

Literature

Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy

Szczepankiewicz, B.G., Liu, G., Hajduk, P.J., Abad-Zapatero, C., Pei, Z., Xin, Z., Lubben, T., Trevillyan, J.M., Stashko, M.A., Ballaron, S.J., Liang, H., Huang, F., Hutchins, C.W., Fesik, S.W., Jirousek, M.R.

(2003) J.Am.Chem.Soc. 125: 4087-4096

• PubMed: 12670229 
• DOI: 10.1021/ja0296733
• Primary Citation of Related Structures:  
  1NO6, 1NNY


• PubMed Abstract: 
  

Protein tyrosine phosphatase 1B (PTP1B) is an enzyme that downregulates the insulin receptor. Inhibition of PTP1B is expected to improve insulin action, and the design of small molecule PTP1B inhibitors to treat type II diabetes has received considerable attention. In this work, NMR-based screening identified a nonselective competitive inhibitor of PTP1B. A second site ligand was also identified by NMR-based screening and then linked to the catalytic site ligand by rational design. X-ray data confirmed that the inhibitor bound with the catalytic site in the native, "open" conformation. The final compound displayed excellent potency and good selectivity over many other phosphatases. The modular approach to drug design described in this work should be applicable for the design of potent and selective inhibitors of other therapeutically relevant protein tyrosine phosphatases.

---

Organizational Affiliation: 

Metabolic Disease Research, Global Pharmaceutical Research and Development Organization, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein-tyrosine 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) Go to Gene View: PTPN1 Go to UniProtKB:  P18031

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
989	A	2-{[4-(2-ACETYLAMINO-2-PENTYLCARBAMOYL-ETHYL)-NAPHTHALEN-1-YL]-OXALYL-AMINO}-BENZOIC ACID COMPOUND 12, N-ACETYL-4-[(CARBOXYCARBONYL)(2-CARBOXYPHENYL)AMINO]-N-PENTYL-1-NAPTHYLALANIAMIDE C29 H31 N3 O7 UESXELNYBIOROE-QHCPKHFHSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
989	Ki: 631 - 1100 nM (100) BINDINGDB
989	Ki: 1100 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.247 
• R-Value Work: 0.192 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 88.730	α = 90.00
b = 88.730	β = 90.00
c = 105.910	γ = 120.00

Software Package:

Software Name	Purpose
MAR345	data collection
CNX	phasing
CNX	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-06 
• Released Date: 2003-04-08 
• Deposition Author(s): Szczepankiewicz, B.G., Liu, G., Hajduk, P.J., Abad-Zapatero, C., Pei, Z., Xin, Z., Lubben, T., Trevillyan, J.M., Stashko, M.A., Ballaron, S.J., Liang, H., Huang, F., Hutchins, C.W., Fesik, S.W., Jirousek, M.R.

Revision History 

• Version 1.0: 2003-04-08
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description