4P58 | pdb_00004p58

Crystal structure of mouse comt bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4P58/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-15 Released: 2014-06-25 
• Deposition Author(s): Lanier, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.199 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.145 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

A fragment-based approach to identifying S-adenosyl-l-methionine -competitive inhibitors of catechol O-methyl transferase (COMT).

Lanier, M., Ambrus, G., Cole, D.C., Davenport, R., Ellery, J., Fosbeary, R., Jennings, A.J., Kadotani, A., Kamada, Y., Kamran, R., Matsumoto, S., Mizukami, A., Okubo, S., Okada, K., Saikatendu, K., Walsh, L., Wu, H., Hixon, M.S.

(2014) J Med Chem 57: 5459-5463

• PubMed: 24847974 
• DOI: https://doi.org/10.1021/jm500475k
• Primary Citation Related Structures: 
  4P58


• PubMed Abstract: 
  

  Catechol O-methyl transferase belongs to the diverse family of S-adenosyl-l-methionine transferases. It is a target involved in the treatment of Parkinson's disease. Here we present a fragment-based screening approach to discover noncatechol derived COMT inhibitors which bind at the SAM binding pocket. We describe the identification and characterization of a series of highly ligand efficient SAM competitive bisaryl fragments (LE = 0.33-0.58). We also present the first SAM-competitive small-molecule COMT co-complex crystal structure.

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Organizational Affiliation: 
• Medicinal Chemistry, ‡Structural Biology, §Discovery Biology, ∥Analytical Chemistry, Takeda California Inc. , 10410 Science Center Drive San Diego California 92121, United States.

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: 24 kDa 
• Atom Count: 1,784 
• Modeled Residue Count: 205 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	212	Mus musculus	Mutation(s): 0  Gene Names: Comt, Comt1 EC: 2.1.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for O88587 (Mus musculus) Explore O88587  Go to UniProtKB:  O88587
IMPC:  MGI:88470

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2F6	B [auth A]	1',3'-dimethyl-1H,1'H-3,4'-bipyrazole C8 H10 N4 LNJKDWJFZASOPC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.199 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.145 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.584	α = 90
b = 98.584	β = 90
c = 115.104	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Lanier, M.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary