5P90 | pdb_00005p90

humanized rat catechol O-methyltransferase in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[(E)-5-pyrrolo[3,2-c]pyridin-1-ylpent-3-enyl]benzamide at 1.24A

• PDB DOI: https://doi.org/10.2210/pdb5P90/pdb
• Deposition Group: G_1002009 ExploreG_1002009

• Classification: TRANSFERASE/TRANSFERASE inhibitor
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-08-29 Released: 2017-08-30 
• Deposition Author(s): Ehler, A., Lerner, C., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: other

Literature

Crystal Structure of a COMT complex

Lerner, C., Rudolph, M.G.

To be published.

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: 25.88 kDa 
• Atom Count: 2,115 
• Modeled Residue Count: 214 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	221	Rattus norvegicus	Mutation(s): 2  Gene Names: Comt EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus) Explore P22734  Go to UniProtKB:  P22734

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
769	E [auth A]	5-(4-fluorophenyl)-2,3-dihydroxy-N-[(E)-5-pyrrolo[3,2-c]pyridin-1-ylpent-3-enyl]benzamide C25 H22 F N3 O3 MYCHLIVPJDYHPD-HNQUOIGGSA-N
NHE	G [auth A], H [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
D1D	F [auth A]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-QWWZWVQMSA-N
PO4	I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	C [auth A], D [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: 1.24 Å
• R-Value Free:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.83	α = 90
b = 54.141	β = 90
c = 81.199	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Ehler, A., Lerner, C., Rudolph, M.G.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Structure summary
• Version 1.2: 2021-11-17
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-04-03
  Changes: Data collection, Refinement description