6XVF

Crystal structure of bovine cytochrome bc1 in complex with tetrahydro-quinolone inhibitor JAG021


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Potent Tetrahydroquinolone Eliminates Apicomplexan Parasites.

McPhillie, M.J.Zhou, Y.Hickman, M.R.Gordon, J.A.Weber, C.R.Li, Q.Lee, P.J.Amporndanai, K.Johnson, R.M.Darby, H.Woods, S.Li, Z.H.Priestley, R.S.Ristroph, K.D.Biering, S.B.El Bissati, K.Hwang, S.Hakim, F.E.Dovgin, S.M.Lykins, J.D.Roberts, L.Hargrave, K.Cong, H.Sinai, A.P.Muench, S.P.Dubey, J.P.Prud'homme, R.K.Lorenzi, H.A.Biagini, G.A.Moreno, S.N.Roberts, C.W.Antonyuk, S.V.Fishwick, C.W.G.McLeod, R.

(2020) Front Cell Infect Microbiol 10: 203-203

  • DOI: https://doi.org/10.3389/fcimb.2020.00203
  • Primary Citation of Related Structures:  
    6XVF

  • PubMed Abstract: 

    Apicomplexan infections cause substantial morbidity and mortality, worldwide. New, improved therapies are needed. Herein, we create a next generation anti-apicomplexan lead compound, JAG21, a tetrahydroquinolone, with increased sp3-character to improve parasite selectivity. Relative to other cytochrome b inhibitors, JAG21 has improved solubility and ADMET properties, without need for pro-drug. JAG21 significantly reduces Toxoplasma gondii tachyzoites and encysted bradyzoites in vitro , and in primary and established chronic murine infections. Moreover, JAG21 treatment leads to 100% survival. Further, JAG21 is efficacious against drug-resistant Plasmodium falciparum in vitro . Causal prophylaxis and radical cure are achieved after P. berghei sporozoite infection with oral administration of a single dose (2.5 mg/kg) or 3 days treatment at reduced dose (0.625 mg/kg/day), eliminating parasitemia, and leading to 100% survival. Enzymatic, binding, and co-crystallography/pharmacophore studies demonstrate selectivity for apicomplexan relative to mammalian enzymes. JAG21 has significant promise as a pre-clinical candidate for prevention, treatment, and cure of toxoplasmosis and malaria.


  • Organizational Affiliation

    School of Chemistry, The University of Leeds, Leeds, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrial445Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P31800 (Bos taurus)
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UniProt GroupP31800
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrial418Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23004 (Bos taurus)
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UniProt GroupP23004
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b378Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00157
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial239Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00125 (Bos taurus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial196Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
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UniProt GroupP13272
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7100Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 874Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrial64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00126 (Bos taurus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial46Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
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UniProt GroupP13272
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 959Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
AA [auth D],
FA [auth E],
N [auth A],
U [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PEE
Query on PEE

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EA [auth E],
V [auth C]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
PX4
Query on PX4

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CA [auth E]1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
HEC
Query on HEC

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Y [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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P [auth C],
Q [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT
Query on LMT

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R [auth C]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
JAG (Subject of Investigation/LOI)
Query on JAG

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W [auth C]2-methyl-3-[4-[4-(trifluoromethyloxy)phenoxy]phenyl]-5,6,7,8-tetrahydro-3~{H}-quinolin-4-one
C23 H20 F3 N O3
VUKDUSVBXDIIJP-OAQYLSRUSA-N
6PE
Query on 6PE

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L [auth A]1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C17 H33 N O8 P
PELYUHWUVHDSSU-OAHLLOKOSA-M
PG4
Query on PG4

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K [auth A],
S [auth C],
T [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES
Query on FES

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BA [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PO4
Query on PO4

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DA [auth E]
GA [auth F]
HA [auth G]
IA [auth G]
JA [auth G]
DA [auth E],
GA [auth F],
HA [auth G],
IA [auth G],
JA [auth G],
M [auth A],
O [auth B],
X [auth C],
Z [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.869α = 90
b = 209.869β = 90
c = 342.418γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
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: 2020-07-22
    Type: Initial release
  • Version 2.0: 2024-01-24
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary