3AEA

Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Dimethylaminomethyl-phenyl)-2-trifluoromethyl-benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial622Sus scrofaMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q0QF01 (Sus scrofa)
Explore Q0QF01 
Go to UniProtKB:  Q0QF01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QF01
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial252Sus scrofaMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q007T0 (Sus scrofa)
Explore Q007T0 
Go to UniProtKB:  Q007T0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ007T0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial140Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWV4 (Sus scrofa)
Explore D0VWV4 
Go to UniProtKB:  D0VWV4
Entity Groups  
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UniProt GroupD0VWV4
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, mitochondrial103Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A5GZW8 (Sus scrofa)
Explore A5GZW8 
Go to UniProtKB:  A5GZW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5GZW8
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 
E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
EPH
Query on EPH

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L [auth D]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 
J [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4

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H [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F9A
Query on F9A

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K [auth D]N-{3-[(dimethylamino)methyl]phenyl}-2-(trifluoromethyl)benzamide
C17 H17 F3 N2 O
JOBMMUWJHLRXCZ-UHFFFAOYSA-N
F3S
Query on F3S

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

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G [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
F [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.505α = 90
b = 83.751β = 90
c = 294.959γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-08-05
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary