5P9N

humanized rat COMT in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[[3-[hydroxy-(1-methylindazol-5-yl)methyl]phenyl]methyl]benzamide at 1.17A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of a COMT complex

Lerner, C.Jakob-Roetne, R.Groebke-Zbinden, K.Buettelmann, B.Rudolph, M.G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catechol O-methyltransferase221Rattus norvegicusMutation(s): 2 
Gene Names: Comt
EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus)
Explore P22734 
Go to UniProtKB:  P22734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22734
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8JE
Query on 8JE

Download Ideal Coordinates CCD File 
I [auth A]5-(4-fluorophenyl)-~{N}-[[3-[(~{S})-(1-methylindazol-5-yl)-oxidanyl-methyl]phenyl]methyl]-2,3-bis(oxidanyl)benzamide
C29 H24 F N3 O4
AYTCJOWSEKPFCS-MHZLTWQESA-N
7JE
Query on 7JE

Download Ideal Coordinates CCD File 
H [auth A]5-(4-fluorophenyl)-~{N}-[[3-[(~{R})-(1-methylindazol-5-yl)-oxidanyl-methyl]phenyl]methyl]-2,3-bis(oxidanyl)benzamide
C29 H24 F N3 O4
AYTCJOWSEKPFCS-HHHXNRCGSA-N
NHE
Query on NHE

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E [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
D1D
Query on D1D

Download Ideal Coordinates CCD File 
F [auth A](4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
SO4
Query on SO4

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G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

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C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.966α = 90
b = 54.033β = 90
c = 80.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    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