6LKD

in meso full-length rat KMO in complex with a pyrazoyl benzoic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Full-length in meso structure and mechanism of rat kynurenine 3-monooxygenase inhibition.

Mimasu, S.Yamagishi, H.Kubo, S.Kiyohara, M.Matsuda, T.Yahata, T.Thomson, H.A.Hupp, C.D.Liu, J.Okuda, T.Kakefuda, K.

(2021) Commun Biol 4: 159-159

  • DOI: https://doi.org/10.1038/s42003-021-01666-5
  • Primary Citation of Related Structures:  
    6LKD, 6LKE

  • PubMed Abstract: 

    The structural mechanisms of single-pass transmembrane enzymes remain elusive. Kynurenine 3-monooxygenase (KMO) is a mitochondrial protein involved in the eukaryotic tryptophan catabolic pathway and is linked to various diseases. Here, we report the mammalian full-length structure of KMO in its membrane-embedded form, complexed with compound 3 (identified internally) and compound 4 (identified via DNA-encoded chemical library screening) at 3.0 Å resolution. Despite predictions suggesting that KMO has two transmembrane domains, we show that KMO is actually a single-pass transmembrane protein, with the other transmembrane domain lying laterally along the membrane, where it forms part of the ligand-binding pocket. Further exploration of compound 3 led to identification of the brain-penetrant compound, 5. We show that KMO is dimeric, and that mutations at the dimeric interface abolish its activity. These results will provide insight for the drug discovery of additional blood-brain-barrier molecules, and help illuminate the complex biology behind single-pass transmembrane enzymes.


  • Organizational Affiliation

    Drug Discovery Research, Astellas Pharma. Inc., Tsukuba, Ibaraki, Japan. shinya.mimasu@astellas.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kynurenine 3-monooxygenase
A, B
495Rattus norvegicusMutation(s): 0 
Gene Names: Kmo
EC: 1.14.13.9
Membrane Entity: Yes 
UniProt
Find proteins for O88867 (Rattus norvegicus)
Explore O88867 
Go to UniProtKB:  O88867
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88867
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
EGO (Subject of Investigation/LOI)
Query on EGO

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
5-[5-(4-chloranyl-3-fluoranyl-phenyl)-4-methyl-pyrazol-1-yl]-2-phenylmethoxy-benzoic acid
C24 H18 Cl F N2 O3
NWWKXTLGLBRUHA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.97α = 90
b = 63.43β = 113.52
c = 152.42γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description