4D6U image
Entry Detail
PDB ID:
4D6U
Keywords:
Title:
Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2014-11-14
Release Date:
2015-01-14
Method Details:
Experimental Method:
Resolution:
4.09 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 65
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
Chain IDs:A
Chain Length:480
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
Chain IDs:B
Chain Length:453
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B
Chain IDs:C, M (auth: P)
Chain Length:379
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
Chain IDs:D, N (auth: Q)
Chain Length:325
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
Chain IDs:E, I, O (auth: R)
Chain Length:274
Number of Molecules:3
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 7
Chain IDs:F, P (auth: S)
Chain Length:111
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 8
Chain IDs:G, Q (auth: T)
Chain Length:82
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
Chain IDs:H, R (auth: U)
Chain Length:91
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 9
Chain IDs:J, T (auth: W)
Chain Length:64
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
Chain IDs:K (auth: N)
Chain Length:480
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
Chain IDs:L (auth: O)
Chain Length:453
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Description:CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
Chain IDs:S (auth: V)
Chain Length:274
Number of Molecules:1
Biological Source:BOS TAURUS
Primary Citation
Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome Bc1.
Proc.Natl.Acad.Sci.USA 112 755 ? (2015)
PMID: 25564664 DOI: 10.1073/PNAS.1416611112

Abstact

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.

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