5MZI | pdb_00005mzi

Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with 3-(5-chloro-6-cyclopropoxy-2-oxo-2,3-dihydro-1,3-benzoxazol-3-yl)propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.194 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5MZI

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Development of a Series of Kynurenine 3-Monooxygenase Inhibitors Leading to a Clinical Candidate for the Treatment of Acute Pancreatitis.

Walker, A.L.Ancellin, N.Beaufils, B.Bergeal, M.Binnie, M.Bouillot, A.Clapham, D.Denis, A.Haslam, C.P.Holmes, D.S.Hutchinson, J.P.Liddle, J.McBride, A.Mirguet, O.Mowat, C.G.Rowland, P.Tiberghien, N.Trottet, L.Uings, I.Webster, S.P.Zheng, X.Mole, D.J.

(2017) J Med Chem 60: 3383-3404

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00055
  • Primary Citation Related Structures: 
    5MZC, 5MZI, 5MZK

  • PubMed Abstract: 

    Recently, we reported a novel role for KMO in the pathogenesis of acute pancreatitis (AP). A number of inhibitors of kynurenine 3-monooxygenase (KMO) have previously been described as potential treatments for neurodegenerative conditions and particularly for Huntington's disease. However, the inhibitors reported to date have insufficient aqueous solubility relative to their cellular potency to be compatible with the intravenous (iv) dosing route required in AP. We have identified and optimized a novel series of high affinity KMO inhibitors with favorable physicochemical properties. The leading example is exquisitely selective, has low clearance in two species, prevents lung and kidney damage in a rat model of acute pancreatitis, and is progressing into preclinical development.


  • Organizational Affiliation
    • Discovery Partnerships with Academia, GlaxoSmithKline , Gunnels Wood Road, Stevenage SG1 2NY, UK.

Macromolecule Content 

  • Total Structure Weight: 104.79 kDa 
  • Atom Count: 7,961 
  • Modeled Residue Count: 899 
  • Deposited Residue Count: 922 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kynurenine 3-monooxygenase
A, B
461Pseudomonas fluorescensMutation(s): 2 
Gene Names: kmoqbsG
EC: 1.14.13.9
UniProt
Find proteins for Q84HF5 (Pseudomonas fluorescens)
Explore Q84HF5 
Go to UniProtKB:  Q84HF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84HF5
Sequence Annotations
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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],
I [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FYK

Query on FYK



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B]
3-(5-chloro-6-cyclopropoxy-2-oxo-2,3-dihydro-1,3-benzoxazol-3-yl)propanoic acid
C13 H12 Cl N O5
AYXQPTCYJAJHBG-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.194 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.58α = 90
b = 52.97β = 103.87
c = 136.14γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-04-19 
  • Deposition Author(s): Rowland, P.

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references