4D6T

Cytochrome bc1 bound to the 4(1H)-pyridone GW844520


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome Bc1.

Capper, M.J.O'Neill, P.M.Fisher, N.Strange, R.W.Moss, D.Ward, S.A.Berry, N.G.Lawrenson, A.S.Hasnain, S.S.Biagini, G.A.Antonyuk, S.V.

(2015) Proc.Natl.Acad.Sci.USA 112: 755

  • DOI: 10.1073/pnas.1416611112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome bc1 is a proven drug target in the prevention and treatment of malaria. The rise in drug-resistant strains of Plasmodium falciparum, the organism responsible for malaria, has generated a global effort in designing new classes of drugs. Muc ...

    Cytochrome bc1 is a proven drug target in the prevention and treatment of malaria. The rise in drug-resistant strains of Plasmodium falciparum, the organism responsible for malaria, has generated a global effort in designing new classes of drugs. Much of the design/redesign work on overcoming this resistance has been focused on compounds that are presumed to bind the Q(o) site (one of two potential binding sites within cytochrome bc1 using the known crystal structure of this large membrane-bound macromolecular complex via in silico modeling. Cocrystallization of the cytochrome bc1 complex with the 4(1H)-pyridone class of inhibitors, GSK932121 and GW844520, that have been shown to be potent antimalarial agents in vivo, revealed that these inhibitors do not bind at the Q(o) site but bind at the Q(i )site. The discovery that these compounds bind at the Q(i) site may provide a molecular explanation for the cardiotoxicity and eventual failure of GSK932121 in phase-1 clinical trial and highlight the need for direct experimental observation of a compound bound to a target site before chemical optimization and development for clinical trials. The binding of the 4(1H)-pyridone class of inhibitors to Q(i) also explains the ability of this class to overcome parasite Q(o)-based atovaquone resistance and provides critical structural information for future design of new selective compounds with improved safety profiles.


    Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom;,Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; s.s.hasnain@liverpool.ac.uk antonyuk@liverpool.ac.uk biagini@liverpool.ac.uk.,Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom s.s.hasnain@liverpool.ac.uk antonyuk@liverpool.ac.uk biagini@liverpool.ac.uk.,Department of Chemistry, Faculty of Science and Engineering, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
A, N
480Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Find proteins for P31800 (Bos taurus)
Go to Gene View: UQCRC1
Go to UniProtKB:  P31800
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
B
453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Find proteins for P23004 (Bos taurus)
Go to Gene View: UQCRC2
Go to UniProtKB:  P23004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B
C, P
379Bos taurusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P00157 (Bos taurus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P00157
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
D, Q
265Bos taurusMutation(s): 0 
Gene Names: CYC1
Find proteins for P00125 (Bos taurus)
Go to Gene View: CYC1
Go to UniProtKB:  P00125
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
E, I, R
274Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 7
F, S
111Bos taurusMutation(s): 0 
Gene Names: UQCRB
Find proteins for P00129 (Bos taurus)
Go to Gene View: UQCRB
Go to UniProtKB:  P00129
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 8
G, T
82Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Find proteins for P13271 (Bos taurus)
Go to Gene View: UQCRQ
Go to UniProtKB:  P13271
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
H, U
91Bos taurusMutation(s): 0 
Gene Names: UQCRH
Find proteins for P00126 (Bos taurus)
Go to Gene View: UQCRH
Go to UniProtKB:  P00126
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 9
J, W
64Bos taurusMutation(s): 0 
Gene Names: UQCR10
Find proteins for P00130 (Bos taurus)
Go to Gene View: UQCR10
Go to UniProtKB:  P00130
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
O
453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Find proteins for P23004 (Bos taurus)
Go to Gene View: UQCRC2
Go to UniProtKB:  P23004
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
V
274Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
C, D, E, F, N, Q, S
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CDL
Query on CDL

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D, G, Q, T
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
GOL
Query on GOL

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R
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C, P
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

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D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
4X9
Query on 4X9

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C, P
3-chloro-2,6-dimethyl-5-{4-[4-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol
C20 H15 Cl F3 N O3
BZRPOJGQEWLGMP-UHFFFAOYSA-N
 Ligand Interaction
PEE
Query on PEE

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C, D, P, Q
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 129.896α = 90.00
b = 129.896β = 90.00
c = 722.152γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Database references