4YSX

Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with the specific inhibitor NN23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

Inaoka, D.K.Shiba, T.Sato, D.Balogun, E.O.Sasaki, T.Nagahama, M.Oda, M.Matsuoka, S.Ohmori, J.Honma, T.Inoue, M.Kita, K.Harada, S.

(2015) Int J Mol Sci 16: 15287-15308

  • DOI: https://doi.org/10.3390/ijms160715287
  • Primary Citation of Related Structures:  
    3ABV, 3AE7, 3AE9, 3AEA, 4YSX, 4YSY, 4YSZ, 4YT0, 4YTM, 4YTP, 4YXD, 5C2T

  • PubMed Abstract: 

    Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs.


  • Organizational Affiliation

    Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan. danielken@m.u-tokyo.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase flavoprotein
A, E
645Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q33862 (Ascaris suum)
Explore Q33862 
Go to UniProtKB:  Q33862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ33862
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
B, F
282Ascaris suumMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for O44074 (Ascaris suum)
Explore O44074 
Go to UniProtKB:  O44074
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO44074
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-large subunit
C, G
188Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92506 (Ascaris suum)
Explore P92506 
Go to UniProtKB:  P92506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92506
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D, H
156Ascaris suumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92507 (Ascaris suum)
Explore P92507 
Go to UniProtKB:  P92507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92507
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
J [auth A],
R [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
EPH
Query on EPH

Download Ideal Coordinates CCD File 
P [auth D],
X [auth H]
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
O [auth C],
V [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4

Download Ideal Coordinates CCD File 
L [auth B],
T [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
E23
Query on E23

Download Ideal Coordinates CCD File 
N [auth B],
W [auth G]
N-(4-tert-butylbenzyl)-2-(trifluoromethyl)benzamide
C19 H20 F3 N O
RYYHDFPDKHYSSE-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
M [auth B],
U [auth F]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
K [auth B],
S [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth E]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
E23 Binding MOAD:  4YSX IC50: 5.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.2α = 90
b = 127.909β = 90
c = 220.546γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description