5NMI | pdb_00005nmi

Cytochrome bc1 bound to the inhibitor MJM170


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.248 (Depositor) 
  • R-Value Observed: 
    0.249 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 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 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
    • University of Leeds, Leeds, UK.

Macromolecule Content 

  • Total Structure Weight: 549.47 kDa 
  • Atom Count: 31,648 
  • Modeled Residue Count: 3,934 
  • Deposited Residue Count: 4,794 
  • Unique protein chains: 10

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
Find proteins for P31800 (Bos taurus)
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UniProt GroupP31800
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Reference Sequence
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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
Find proteins for P23004 (Bos taurus)
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Reference Sequence
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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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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
O [auth Q]
240Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P00125 (Bos taurus)
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UniProt GroupP00125
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Reference Sequence
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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 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
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UniProt GroupP13272
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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
Find proteins for P00130 (Bos taurus)
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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
CA [auth D],
OA [auth Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.248 (Depositor) 
  • R-Value Observed: 0.249 (Depositor) 
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
  • Version 2.0: 2025-04-09
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary