3TGU

Cytochrome bc1 complex from chicken with pfvs-designed moa inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

Starting Model: experimental
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Literature

Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex.

Hao, G.F.Wang, F.Li, H.Zhu, X.L.Yang, W.C.Huang, L.S.Wu, J.W.Berry, E.A.Yang, G.F.

(2012) J Am Chem Soc 134: 11168-11176

  • DOI: https://doi.org/10.1021/ja3001908
  • Primary Citation of Related Structures:  
    3TGU

  • PubMed Abstract: 

    A critical challenge to the fragment-based drug discovery (FBDD) is its low-throughput nature due to the necessity of biophysical method-based fragment screening. Herein, a method of pharmacophore-linked fragment virtual screening (PFVS) was successfully developed. Its application yielded the first picomolar-range Q(o) site inhibitors of the cytochrome bc(1) complex, an important membrane protein for drug and fungicide discovery. Compared with the original hit compound 4 (K(i) = 881.80 nM, porcine bc(1)), the most potent compound 4f displayed 20 507-fold improved binding affinity (K(i) = 43.00 pM). Compound 4f was proved to be a noncompetitive inhibitor with respect to the substrate cytochrome c, but a competitive inhibitor with respect to the substrate ubiquinol. Additionally, we determined the crystal structure of compound 4e (K(i) = 83.00 pM) bound to the chicken bc(1) at 2.70 Å resolution, providing a molecular basis for understanding its ultrapotency. To our knowledge, this study is the first application of the FBDD method in the discovery of picomolar inhibitors of a membrane protein. This work demonstrates that the novel PFVS approach is a high-throughput drug discovery method, independent of biophysical screening techniques.


  • Organizational Affiliation

    Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein iA,
K [auth N]
446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2B,
L [auth O]
441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC,
M [auth P]
380Gallus gallusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP18946
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial cytochrome c1, heme proteinD,
N [auth Q]
241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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UniProt GroupD0VX26
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
O [auth R]
196Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome c reductase 14 kda proteinF,
P [auth S]
110Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-cG,
Q [auth T]
81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viiiH,
R [auth U]
77Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI,
S [auth V]
76Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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UniProt GroupQ5ZLR5
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda proteinJ,
T [auth W]
61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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IA [auth G],
QA [auth P],
UA [auth Q],
Z [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ
Query on UQ

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PA [auth P],
Y [auth C]
Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
PEE
Query on PEE

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AA [auth C]
BA [auth C]
HA [auth E]
KA [auth N]
RA [auth P]
AA [auth C],
BA [auth C],
HA [auth E],
KA [auth N],
RA [auth P],
YA [auth R]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC

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

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LA [auth P],
MA [auth P],
V [auth C],
W [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
WF3
Query on WF3

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OA [auth P],
X [auth C]
methyl (2E)-3-methoxy-2-[2-({[6-methyl-3-(trifluoromethyl)quinoxalin-2-yl]oxy}methyl)phenyl]prop-2-enoate
C22 H19 F3 N2 O4
GJLNLJPTCNQCFH-FOWTUZBSSA-N
BOG
Query on BOG

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EA [auth D],
FA [auth D],
NA [auth P],
VA [auth Q],
WA [auth Q]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FES
Query on FES

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GA [auth E],
XA [auth R]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL
Query on GOL

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CA [auth C],
SA [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNL
Query on UNL

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JA [auth N],
U [auth A]
Unknown ligand
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
C,
M [auth P]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.678α = 90
b = 183.305β = 90
c = 241.944γ = 90
Software Package:
Software NamePurpose
Adxvdata processing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.0: 2023-09-13
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary