3AE9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 ...

    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 Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan. harada@kit.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial622Sus scrofaMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial252Sus scrofaMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial140Sus scrofaMutation(s): 0 
Gene Names: SDHC
Membrane Entity: Yes 
UniProt
Find proteins for D0VWV4 (Sus scrofa)
Explore D0VWV4 
Go to UniProtKB:  D0VWV4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWV4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial103Sus scrofaMutation(s): 0 
Gene Names: SDHD
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / 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
 Ligand Interaction
EPH
Query on EPH

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

Download Ideal Coordinates CCD File 
J [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FD8
Query on FD8

Download Ideal Coordinates CCD File 
K [auth C]N-[3-(pentafluorophenoxy)phenyl]-2-(trifluoromethyl)benzamide
C20 H9 F8 N O2
ZTJJBXFGRJEBCQ-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
H [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
I [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
G [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.609α = 90
b = 84.249β = 90
c = 295.646γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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