5P90

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of a COMT complex

Lerner, C.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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
769
Query on 769

Download Ideal Coordinates CCD File 
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
Query on NHE

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

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F [auth A](4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
PO4
Query on PO4

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I [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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: 1.24 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.83α = 90
b = 54.141β = 90
c = 81.199γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
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: 2017-08-30
    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