6HAW

Crystal structure of bovine cytochrome bc1 in complex with 2-pyrazolyl quinolone inhibitor WDH2G7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Potent Antimalarial 2-Pyrazolyl Quinolonebc1(Qi) Inhibitors with Improved Drug-like Properties.

David Hong, W.Leung, S.C.Amporndanai, K.Davies, J.Priestley, R.S.Nixon, G.L.Berry, N.G.Samar Hasnain, S.Antonyuk, S.Ward, S.A.Biagini, G.A.O'Neill, P.M.

(2018) ACS Med Chem Lett 9: 1205-1210

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00371
  • Primary Citation of Related Structures:  
    6HAW

  • PubMed Abstract: 

    A series of 2-pyrazolyl quinolones has been designed and synthesized in 5-7 steps to optimize for both in vitro antimalarial potency and various in vitro drug metabolism and pharmacokinetics (DMPK) features. The most potent compounds display no cross-resistance with multidrug resistant parasite strains (W2) compared to drug sensitive strains (3D7), with IC 50 (concentration of drug required to achieve half maximal growth suppression) values in the range of 15-33 nM. Furthermore, members of the series retain moderate activity against the atovaquone-resistant parasite isolate (TM90C2B). The described 2-pyrazoyl series displays improved DMPK properties, including improved aqueous solubility compared to previously reported quinolone series and acceptable safety margin through in vitro cytotoxicity assessment. The 2-pyrazolyl quinolones are believed to bind to the ubiquinone-reducing Q i site of the parasite bc 1 complex, which is supported by crystallographic studies of bovine cytochrome bc 1 complex.


  • Organizational Affiliation

    Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, U.K.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrial438Bos taurusMutation(s): 0 
UniProt
Find proteins for P31800 (Bos taurus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrial413Bos taurusMutation(s): 0 
UniProt
Find proteins for P23004 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b378Bos taurusMutation(s): 0 
UniProt
Find proteins for P00157 (Bos taurus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial239Bos taurusMutation(s): 0 
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: 1.10.2.2
UniProt
Find proteins for P13272 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 799Bos taurusMutation(s): 0 
UniProt
Find proteins for P00129 (Bos taurus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 874Bos taurusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrial64Bos taurusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial46Bos taurusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P13272 (Bos taurus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 959Bos taurusMutation(s): 0 
UniProt
Find proteins for P00130 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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

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JA [auth E],
X [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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HA [auth E]1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
PX6
Query on PX6

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CA [auth C],
S [auth B]
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
C35 H68 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-M
HEC
Query on HEC

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

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

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V [auth C]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FX2 (Subject of Investigation/LOI)
Query on FX2

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Y [auth C]7-methoxy-3-methyl-2-[1-[[4-(trifluoromethyloxy)phenyl]methyl]pyrazol-4-yl]-3~{H}-quinolin-4-one
C22 H18 F3 N3 O3
MHUJCWZTTGWJRK-ZDUSSCGKSA-N
6PE
Query on 6PE

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K [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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R [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES
Query on FES

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

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AA [auth C],
BA [auth C],
L [auth A],
Z [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
Query on PO4

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EA [auth D]
IA [auth E]
LA [auth F]
M [auth A]
MA [auth F]
EA [auth D],
IA [auth E],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
NA [auth G],
O [auth A],
OA [auth G],
PA [auth G],
Q [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.69α = 90
b = 212.69β = 90
c = 347.066γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 2.0: 2024-01-17
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary