3TGU image
Deposition Date 2011-08-17
Release Date 2012-07-04
Last Version Date 2023-09-13
Entry Detail
PDB ID:
3TGU
Title:
Cytochrome bc1 complex from chicken with pfvs-designed moa inhibitor bound
Biological Source:
Source Organism:
Gallus gallus (Taxon ID: 9031)
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.28
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i
Chain IDs:A, K (auth: N)
Chain Length:446
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2
Chain IDs:B, L (auth: O)
Chain Length:441
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b
Gene (Uniprot):MT-CYB
Chain IDs:C, M (auth: P)
Chain Length:380
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Mitochondrial cytochrome c1, heme protein
Chain IDs:D, N (auth: Q)
Chain Length:241
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit Rieske, mitochondrial
Gene (Uniprot):UQCRFS1
Chain IDs:E, O (auth: R)
Chain Length:196
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein
Chain IDs:F, P (auth: S)
Chain Length:110
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
Chain IDs:G, Q (auth: T)
Chain Length:81
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii
Chain IDs:H, R (auth: U)
Chain Length:77
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit Rieske, mitochondrial
Gene (Uniprot):UQCRFS1
Chain IDs:I, S (auth: V)
Chain Length:76
Number of Molecules:2
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Molecule:Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein
Chain IDs:J, T (auth: W)
Chain Length:61
Number of Molecules:2
Biological Source:Gallus gallus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME C MET N-FORMYLMETHIONINE
Primary Citation
Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex.
J.Am.Chem.Soc. 134 11168 11176 (2012)
PMID: 22690928 DOI: 10.1021/ja3001908

Abstact

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.

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