5NMI

Cytochrome bc1 bound to the inhibitor MJM170


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections.

McPhillie, M.Zhou, Y.El Bissati, K.Dubey, J.Lorenzi, H.Capper, M.Lukens, A.K.Hickman, M.Muench, S.Verma, S.K.Weber, C.R.Wheeler, K.Gordon, J.Sanders, J.Moulton, H.Wang, K.Kim, T.K.He, Y.Santos, T.Woods, S.Lee, P.Donkin, D.Kim, E.Fraczek, L.Lykins, J.Esaa, F.Alibana-Clouser, F.Dovgin, S.Weiss, L.Brasseur, G.Wirth, D.Kent, M.Hood, L.Meunieur, B.Roberts, C.W.Hasnain, S.S.Antonyuk, S.V.Fishwick, C.McLeod, R.

(2016) Sci Rep 6: 29179

  • DOI: 10.1038/srep29179

  • PubMed Abstract: 
  • Toxoplasma gondii, the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to faci ...

    Toxoplasma gondii, the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to facilitate drug development: EGS strain T. gondii forms cysts in vitro that induce oocysts in cats, the gold standard criterion for cysts. These cysts highly express cytochrome b. Using these models, we envisioned, and then created, novel 4-(1H)-quinolone scaffolds that target the cytochrome bc1 complex Qi site, of which, a substituted 5,6,7,8-tetrahydroquinolin-4-one inhibits active infection (IC50, 30 nM) and cysts (IC50, 4 μM) in vitro, and in vivo (25 mg/kg), and drug resistant Plasmodium falciparum (IC50, <30 nM), with clinically relevant synergy. Mutant yeast and co-crystallographic studies demonstrate binding to the bc1 complex Qi site. Our results have direct impact on improving outcomes for those with toxoplasmosis, malaria, and ~2 billion persons chronically infected with encysted bradyzoites.


    Organizational Affiliation

    University of Leeds, Leeds, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A, N
444Bos 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, O
423Bos 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
372Bos 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
240Bos 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, 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
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
ARG-ASN-TRP-VAL-PRO-THR-ALA-GLN-LEU-TRP-GLY-ALA-VAL-GLY-ALA-VAL-GLY-LEU-VAL-SER-ALA-THR
K, X
22Bos taurusMutation(s): 0 
Gene Names: UQCR11 (UQCR)
Find proteins for P07552 (Bos taurus)
Go to Gene View: UQCR11
Go to UniProtKB:  P07552
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download SDF File 
Download CCD File 
C, D, P
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
MJM
Query on MJM

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Download CCD File 
C, P
(4aS)-2-methyl-3-(4-phenoxyphenyl)-5,6,7,8-tetrahydroquinolin-4(4aH)-one
C22 H21 N O2
HIEQRZFLXIDNCA-IBGZPJMESA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
PEE
Query on PEE

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Download CCD File 
C, D, E, P, R
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: 3.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.248 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 129.477α = 90.00
b = 129.477β = 90.00
c = 720.294γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
iMOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Advisory, Data collection, Derived calculations