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 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 U S A 112: 755

  • DOI: 10.1073/pnas.1416611112
  • Primary Citation of Related Structures:  
    4D6T, 4D6U

  • 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. 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 ...

    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; s.s.hasnain@liverpool.ac.uk antonyuk@liverpool.ac.uk biagini@liverpool.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIALA, K [auth N]480Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIALB453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME BC, M [auth P]379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIALD, N [auth Q]265Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALE, I, O [auth R]274Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 7F, P [auth S]111Bos taurusMutation(s): 0 
Gene Names: UQCRB
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 8G, Q [auth T]82Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIALH, R [auth U]91Bos taurusMutation(s): 0 
Gene Names: UQCRH
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 9J, T [auth W]64Bos taurusMutation(s): 0 
Gene Names: UQCR10
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIALL [auth O]453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALS [auth V]274Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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DA [auth D], HA [auth G], PA [auth Q], WA [auth T]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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EA [auth D], NA [auth P], QA [auth Q], Y [auth C]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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OA [auth Q], Z [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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KA [auth P], LA [auth P], U [auth C], V [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
4X9 (Subject of Investigation/LOI)
Query on 4X9

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MA [auth P], W [auth C]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
FES
Query on FES

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TA [auth R]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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AA [auth D] , BA [auth D] , CA [auth D] , FA [auth E] , GA [auth F] , IA [auth N] , JA [auth N] , RA [auth Q] , 
AA [auth D], BA [auth D], CA [auth D], FA [auth E], GA [auth F], IA [auth N], JA [auth N], RA [auth Q], SA [auth Q], VA [auth S], X [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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UA [auth R]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 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 
  • R-Value Observed: 0.208 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.896α = 90
b = 129.896β = 90
c = 722.152γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
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: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Database references