5NMI

Cytochrome bc1 bound to the inhibitor MJM170


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/srep29179
  • Primary Citation of Related Structures:  
    5NMI

  • 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 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

    Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
L [auth N]
444Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP31800
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
M [auth O]
423Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC,
N [auth P]
372Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00157 (Bos taurus)
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UniProt GroupP00157
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
O [auth Q]
240Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00125
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
I,
P [auth R],
T [auth V]
274Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
Q [auth S]
111Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00129 (Bos taurus)
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UniProt GroupP00129
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G,
R [auth T]
82Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13271 (Bos taurus)
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UniProt GroupP13271
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH,
S [auth U]
91Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00126 (Bos taurus)
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UniProt GroupP00126
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J,
U [auth W]
64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-ASN-TRP-VAL-PRO-THR-ALA-GLN-LEU-TRP-GLY-ALA-VAL-GLY-ALA-VAL-GLY-LEU-VAL-SER-ALA-THRK,
V [auth X]
22Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07552 (Bos taurus)
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UniProt GroupP07552
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AA [auth C]
BA [auth C]
EA [auth D]
HA [auth P]
MA [auth P]
AA [auth C],
BA [auth C],
EA [auth D],
HA [auth P],
MA [auth P],
NA [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEE
Query on PEE

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DA [auth D]
GA [auth E]
LA [auth P]
PA [auth R]
QA [auth R]
DA [auth D],
GA [auth E],
LA [auth P],
PA [auth R],
QA [auth R],
Z [auth C]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC

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CA [auth D],
OA [auth Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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IA [auth P],
JA [auth P],
W [auth C],
X [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
MJM
Query on MJM

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KA [auth P],
Y [auth C]
(4aS)-2-methyl-3-(4-phenoxyphenyl)-5,6,7,8-tetrahydroquinolin-4(4aH)-one
C22 H21 N O2
HIEQRZFLXIDNCA-IBGZPJMESA-N
FES
Query on FES

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FA [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.477α = 90
b = 129.477β = 90
c = 720.294γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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