Inhibitor-ligand protease complex | Amino acid residue | Distance (Å) | Type | Binding affinity |
---|---|---|---|---|
34a vs. 5K5M | A:SER763 A:CYS780 :A:SER885 A:ARG773 A:TYR882 A:ASN777 A:TRP833 A:TRP833 A:TYR882 A:HIE786 A:CYS780 A:MET809 | 1.852 1.799 2.084 2.895 5.199 2.668 3.466 3.867 5.027 4.683 4.011 4.448 | C HB C HB C HB C–H-B Pi–Sulfur Pi–Lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi T-shaped Pi-Alkyl Pi-Alkyl Pi-Alkyl | − 26.54 |
34b vs. 5K5M | A: ASN777 A: TRP833 A: SER885 A: SER885 A: MET809 A: MET809 A: CYS780 A: TYR882 A: ASN777 A: TRP833 A: TRP833 A: TYR882 A: HIE786 | 1.858 2.164 1.836 2.123 2.957 2.689 5.877 5.828 2.929 3.565 3.616 4.507 4.157 | C HB C HB C HB C HB Pi–donor hydrogen bond Pi–Sigma Pi–Sulfur Pi–Sulfur Pi–Lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi stacked Pi–alkyl | − 29.612 |
34c vs. 5K5M | A:MET809 A:TRP833 A:MET809 A:MET809 A:CYS780 A:TYR882 A:ASN777 A:TRP833 A:TRP833 A:TYR882 A:HIE786 | 2.370 2.398 2.978 2.669 5.598 5.860 2.797 3.663 3.755 4.385 4.124 | C HB C HB Pi–donor hydrogen bond Pi–sigma Pi–sulfur Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi stacked Pi–alkyl | − 22.652 |
34d vs. 5K5M | A: SER763 A: ARG773 A: SER763 A: TYR882 A: ASN777 A: TRP833 A: TRP833 TYR882 A: HIE786 A: CYS780 A: MET809 | 2.613 2.649 2.251 5.651 2.904 3.524 4.114 4.621 4.352 4.005 4.361 | C HB C HB C HB Pi-Sulfur Pi-Lone Pair Pi-Pi Stacked Pi-Pi Stacked Pi-Pi T-shaped Pi-Alkyl Pi-Alkyl Pi-Alkyl | − 23.644 |
34e vs. 5K5M | A:SER763 A:SER763 A:ARG773 A:TYR882 A:ASN777 A:TRP833 A:TRP833 A:TYR882 A:HIE786 A:CYS780 A:MET809 | 2.609 2.255 2.676 5.643 2.907 3.520 4.111 4.621 4.343 4.002 4.364 | C HB C HB C HB Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi T-shaped Pi–alkyl Pi–alkyl Pi–alkyl | − 23.594 |
34f vs. 5K5M | A: SER763 A: CYS780 A: TRP833 A: ASP808 : RES1:H9 -RES1:N1 : TYR882 A: ASN777 A: TRP833 A: TRP833 A: TYR882 A: HIE786 A: CYS780 A: MET809 | 1.993 1.752 1.733 2.548 2.123 5.320 2.864 3.345 3.786 4.970 4.575 3.966 4.371 | C HB C HB C HB C HB C–H-B Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi T-shaped Pi–alkyl Pi–alkyl Pi–alkyl | − 19.992 |
34 g vs. 5K5M | A:SER763 A:ASN777 A:CYS780 A:SER885 A:SER885 A:CYS780 A:TYR882 A:ASN777 A:TRP833 A:TRP833 A:TYR882 A:HIE786 A:MET809 | 2.041 1.582 1.762 1.937 2.832 2.457 5.305 2.727 3.498 3.904 4.892 4.589 4.436 | C HB C HB C HB C HB C–H-B Pi–donor hydrogen bond Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi T-shaped Pi–alkyl Pi–alkyl | − 23.943 |
34 h vs. 5K5M | A: ASN777 A: TRP833 A: ASN777 A: SER885 A: MET809 A: CYS780 A: TYR882 A: ASN777 A: TYR882 A: TRP833 A: HIE786 A: MET809 A: ALA776 | 1.709 2.161 3.071 2.603 2.841 5.257 5.644 2.633 4.454 4.704 4.215 5.252 5.068 | C HB C HB C HB C HB Pi–donor hydrogen bond Pi–sulfur Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi T-shaped Pi–alkyl Pi–alkyl Pi–alkyl | − 19.292 |
34i vs. 5K5M | A:SER763 A:CYS780 A:TRP833 A:ASP808 :RES1:H9-RES1:N1 A:TYR882 A:ASN777 A:TRP833 A:TRP833 A:TYR882 A:HIE786 A:CYS780 A:MET809 | 1.987 1.738 1.735 2.545 2.119 5.321 2.869 3.338 3.784 4.978 4.548 3.968 4.369 | C HB C HB C HB C HB C–H-B Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi T-shaped Pi–alkyl Pi–alkyl Pi–alkyl | − 20.121 |
34j vs. 5K5M | A: CYS780 A: TRP833 A: ASP808 : RES1:H9 -RES1:N1 A: TYR882 A: ASN777 A: TRP833 A: TRP833 A: TYR882 A: HIE786 A: CYS780 A: MET809 | 1.738 1.735 2.545 2.119 5.322 2.869 3.338 3.7845 4.978 4.549 3.968 4.3692 | C HB C HB C HB C–H-B Pi–sulfur Pi–lone pair Pi–Pi stacked Pi–Pi stacked Pi–Pi T-shaped Pi–alkyl Pi–alkyl Pi–alkyl | − 19.091 |
Co-crystalised ligand vs. 5K5M | A: ARG729 A: THR794 A: TRP795 A: LYS800 A: GLU802 A: THR794 A: SER710 A: CYS709 A: ARG729 A: THR794 A: HIS711 A: LEU512 A: ALA799 | 3.109 2.748 3.399 2.823 2.673 3.336 3.574 3.492 4.150 4.035 5.183 4.182 4.224 | C HB C HB C HB C HB C HB C–H-B C–H-B C–H-B Pi–cation Pi–donor hydrogen bond Pi–Pi T-shaped Alkyl Alkyl | − 25.0433 |
Ribavirin vs. 5K5M | A: LYS756 A: SER763 A: CYS780 A: CYS780 A: ASN777 A: GLN760 A: GLN760 A: THR806 A: THR806 A: SER785 A: THR806 A: GLU807 A: GLN760 A: MET809 A: CYS780 A: MET809 | 1.690 1.853 2.536 2.467 2.799 2.896 2.208 2.554 2.927 2.194 2.056 2.985 2.477 3.115 4.584 4.758 | C HB C HB C HB C HB C HB C HB C HB C HB C–H-B C–H-B C–H-B C–H-B C–H-B Pi–donor hydrogen bond Pi–alkyl Pi–alkyl | − 12.4462 |
SAH vs. 5K5M | A:LYS756 A:ASN777 A:CYS780 A:MET809 :GLN760 A:GLN760 A:SER763 A:ASP808 A:GLN760 A:SER785 A:THR806 A:ASP808 A:HIE786 A:TYR882 A:HIE786 | 2.325 1.871 1.840 2.925 2.099 2.047 2.816 2.398 2.333 2.841 2.385 2.721 2.553 4.328 4.782 | C HB C HB C HB C HB C HB C HB C–H-B C–H-B C–H-B C–H-B C–H-B C–H-B C–H-B Pi–sulfur Pi–Pi T-shaped | − 16.5362 |