Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.68 kDa 
• Atom Count: 8641 
• Modelled Residue Count: 1092 
• Deposited Residue Count: 1272 
• Unique protein chains: 4

4YTP

CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH N-[(4-tert-butylphenyl)methyl]-2-(trifluoromethyl)benzamide

• DOI: 10.2210/pdb4YTP/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2015-03-18 Released: 2015-08-05 
• Deposition Author(s): Harada, S., Shiba, T., Sato, D., Yamamoto, A., Nagahama, M., Yone, A., Inaoka, D.K., Sakamoto, K., Inoue, M., Honma, T., Kita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 

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

• PubMed: 26198225 
• DOI: 10.3390/ijms160715287
• Primary Citation of Related Structures:  
  5C2T, 3ABV, 3AEA, 3AE7, 3AE9, 4YTM, 4YSX, 4YSY, 4YSZ, 4YT0


• 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.

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Organizational Affiliation: 

Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A	664	Sus scrofa	Mutation(s): 0  Gene Names: SDHA EC: 1.3.5.1
Find proteins for Q0QF01 (Sus scrofa) Explore Q0QF01  Go to UniProtKB:  Q0QF01

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	B	280	Sus scrofa	Mutation(s): 0  Gene Names: SDHB EC: 1.3.5.1
Find proteins for Q007T0 (Sus scrofa) Explore Q007T0  Go to UniProtKB:  Q007T0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial	C	169	Sus scrofa	Mutation(s): 0  Gene Names: SDHC
Find proteins for D0VWV4 (Sus scrofa) Explore D0VWV4  Go to UniProtKB:  D0VWV4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D	159	Sus scrofa	Mutation(s): 0  Gene Names: SDHD
Find proteins for A5GZW8 (Sus scrofa) Explore A5GZW8  Go to UniProtKB:  A5GZW8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM	I [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SF4	G [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
E23	J [auth C]	N-(4-tert-butylbenzyl)-2-(trifluoromethyl)benzamide C19 H20 F3 N O RYYHDFPDKHYSSE-UHFFFAOYSA-N
F3S	H [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW
FES	F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.429	α = 90
b = 84.008	β = 90
c = 294.817	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-18 
• Released Date: 2015-08-05 
Deposition Author(s): Harada, S., Shiba, T., Sato, D., Yamamoto, A., Nagahama, M., Yone, A., Inaoka, D.K., Sakamoto, K., Inoue, M., Honma, T., Kita, K.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations