D3Targets-2019-nCoV

D3Docking

Job Title:Ritonavir

Job File:0.mol2

Note:
The 'pml' files in the result should be opened inPyMOL2.

Molecular Descriptors:Molecular Weight: 720.31
Lipid-Water partition: 5.91
Number of Hydrogen Bond Acceptors: 9
Number of Hydrogen Bond Donors: 4
Number of Rotatable Bonds: 17
Number of Heavy Atoms: 50
Number of Aliphatic Rings of a Molecular: 0
Number of Aromatic Rings of a Molecular: 4
Topological Polar Suface Area: 145.78
Druglikeness: Maybe bad

Score:export to excel

Rank	Target Full Name	State	Score	ProteinID	Pocket	Organism	Model Source	Rank^a
1	cGMP-specific 3',5'-cyclic phosphodiesterase		-11.16	O76074	Pocket1	human	PDB	3
2	RAC-alpha serine/threonine-protein kinase		-11.01	P31749	Pocket1	human	PDB	3
3	Mitogen-activated protein kinase 10/c-Jun N-terminal kinase 3		-10.16	P53779	Pocket1	human	PDB	1
4	3C-like proteinase	Dimer	-9.88	QHD43415.1	Pocket2	SARS-CoV-2	PDB	1
5	ORF1ab polyprotein 6453-6798 Uridylate-specific endoribonuclease		-9.83	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
6	ORF1ab polyprotein 5926-6452 Guanine-N7 methyltransferase		-9.61	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	6
7	ORF1ab polyprotein 819-2763 Papain-like proteinase	Dimer	-9.5	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	5
8	Non-structural protein 4		-9.48	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	4
9	Disintegrin and metalloproteinase domain-containing protein 17	+Zn	-9.45	P78536	Pocket1	human		1
10	Eukaryotic initiation factor 4A-I		-9.4	P60842	Pocket2	human	PDB	5
11	Spike protein	Open	-9.4	QHD43416.1	Pocket2	SARS-CoV-2	PDB	4
12	Envelope protein	Pentamer	-9.4	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	1
13	Disintegrin and metalloproteinase domain-containing protein 17		-9.36	P78536	Pocket1	human	Swiss-model	1
14	Complement Component 5	Monomer	-9.35	P01031	Pocket1	human	PDB	3
15	ORF1ab polyprotein 3264-3569 3C-like proteinase	Dimer	-9.26	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
16	Nucleocapsid phosphoprotein	N terminal	-9.2	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	4
17	Non-structural protein 2		-9.12	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	4
18	Spike protein	Closed	-9.1	QHD43416.1	Pocket2	SARS-CoV-2	PDB	4
19	SARS-COV-2 chimeric receptor-binding domain+Angiotensin converting enzyme 2		-9.05	/	Pocket1	human	PDB	2
20	Dihydroorotate dehydrogenase		-9.05	Q02127	Pocket1	human	PDB	22
21	Glycogen synthase kinase-3 beta		-9	P49841	Pocket1	human	PDB	4
22	Mitogen-activated protein kinase 9/c-Jun N-terminal kinase 2		-8.97	P45984	Pocket1	human	Swiss-model	7
23	Complement Component 5	Dimer	-8.97	P01031	Pocket1	human	PDB	5
24	Caveolin-2		-8.95	P51636	Pocket1	human	Robetta	10
25	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase	+Mg	-8.91	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	2
26	ADP ribose phosphatase	Dimer	-8.87	QHD43415.1	Pocket3	SARS-CoV-2	PDB	7
27	Mitogen-activated protein kinase 8/c-Jun N-terminal kinase 1		-8.81	P45983	Pocket1	human	Swiss-model	6
28	ADP ribose phosphatase	Monomer	-8.71	QHD43415.1	Pocket1	SARS-CoV-2	PDB	9
29	Nonstructural protein NS8	Dimer	-8.71	A0A6C0N6C6	Pocket1	SARS-CoV-2	PDB	4
30	Papain-like proteinase	Trimer	-8.69	QHD43415.1	Pocket1	SARS-CoV-2	PDB	5
31	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase		-8.58	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
32	RNA-dependent RNA polymerase	+RNA & +Mg	-8.57	QHD43415.1	Pocket6	SARS-CoV-2	PDB	18
33	Heterogeneous nuclear ribonucleoprotein A1		-8.57	P09651	Pocket1	human	PDB	7
34	Nucleocapsid phosphoprotein	C terminal & Monomer	-8.54	P0DTC9	Pocket1	SARS-CoV-2	PDB	8
35	ORF1ab polyprotein 3264-3569 3C-like proteinase	Monomer	-8.48	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
36	RNA-dependent RNA polymerase		-8.44	QHD43415.1	Pocket2	SARS-CoV-2	PDB	2
37	ORF1ab polyprotein 5325-5925 Helicase	Monomer	-8.43	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	8
38	ORF1ab polyprotein 6799-7096 2'-O-methyltransferase		-8.36	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	3
39	Uridylate-specific endoribonuclease	Dimer	-8.34	QHD43415.1	Pocket3	SARS-CoV-2	PDB	8
40	Uridylate-specific endoribonuclease	Monomer	-8.32	QHD43415.1	Pocket1	SARS-CoV-2	PDB	9
41	ORF1ab 5325-5925 Helicase	Dimer	-8.29	QHD43415.1	Pocket4	SARS-CoV-2	Swiss-model	10
42	Tyrosine-protein kinase ABL2		-8.26	P42684	Pocket1	human	PDB	16
43	Spike protein	Closed	-8.23	QHD43416.1	Pocket5	SARS-CoV-2	Swiss-model	2
44	Non-structural protein 9	Monomer	-8.18	QHD43415.1	Pocket1	SARS-CoV-2	PDB	1
45	ORF1ab polyprotein 819-2763 Papain-like proteinase	Monomer	-8.16	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	10
46	Nucleocapsid phosphoprotein	N terminal & Tetramer	-8.1	QHD43423.2	Pocket1	SARS-CoV-2	PDB	13
47	Complement Component 3		-8.09	P01024	Pocket2	human	PDB	3
48	Angiotensin converting enzyme 2		-8.08	P59594	Pocket1	human	PDB	9
49	RAC-beta serine/threonine-protein kinase		-8.08	P31751	Pocket1	human	PDB	11
50	RNA-dependent RNA polymerase	Only Nsp12 & MD	-8.06	P0DTD1	Pocket2	SARS-CoV-2	Molecular Dynamics	4
51	Transmembrane protease serine 2		-8.04	O15393	Pocket1	human	Robetta	8
52	Spike protein	Open	-8.01	QHD43416.1	Pocket4	SARS-CoV-2	Swiss-model	13
53	2'-O-Methyltransferase		-7.76	P0DTD1	Pocket3	SARS-CoV-2	PDB	3
54	Spike protein S2 subunit		-7.72	/	Pocket1	SARS-CoV-2	PDB	6
55	3C-like proteinase	Monomer	-7.72	QHD43415.1	Pocket5	SARS-CoV-2	PDB	3
56	AP2-associated protein kinase 1		-7.69	Q2M2I8	Pocket5	human	PDB	2
57	Spike protein-heptad repeat 1		-7.69	QHD43416.1	Pocket3	SARS-CoV-2	Swiss-model	4
58	Non-structural protein 6		-7.65	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	11
59	3C-like proteinase	MD	-7.6	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	5
60	Cyclophilin A		-7.59	P62937	Pocket1	human	PDB	6
61	Furin		-7.57	P09958	Pocket1	human	PDB	14
62	Non-structural protein 10		-7.55	P0DTC1	Pocket1	SARS-CoV-2	PDB	6
63	Nonstructural protein NS8	Monomer	-7.53	A0A6C0N6C6	Pocket1	SARS-CoV-2	PDB	2
64	Non-structural protein 9	Dimer	-7.48	QHD43415.1	Pocket3	SARS-CoV-2	PDB	3
65	Nucleocapsid phosphoprotein	C terminal & Dimer	-7.38	P0DTC9	Pocket2	SARS-CoV-2	PDB	5
66	3C-like proteinase	MD	-7.37	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	7
67	Nucleocapsid phosphoprotein	C terminal	-7.27	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	15
68	3C-like proteinase	MD	-7.23	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	8
69	Cathepsin L		-7.18	P07711	Pocket1	human	PDB	4
70	3C-like proteinase	MD	-7.17	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	15
71	Papain-like protease	Monomer	-7.11	QHD43415.1	Pocket2	SARS-CoV-2	PDB	3
72	ORF1ab polyprotein 4254-4392 Non-structural protein 10		-7.09	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	8
73	Non-structural protein 7 + Non-structural protein 8	Complex	-7.09	P0DTC1	Pocket1	SARS-CoV-2	PDB	12
74	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Dimer	-7.04	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	5
75	RAC-gamma serine/threonine-protein kinase		-6.89	Q9Y243	Pocket1	human	PDB	11
76	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Monomer	-6.88	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	11
77	Calnexin		-6.79	P27824	Pocket1	human	Swiss-model	4
78	Nucleocapsid phosphoprotein	N terminal & Monomer	-6.7	QHD43423.2	Pocket1	SARS-CoV-2	PDB	7
79	Calnexin	+Ca	-6.67	P27823	Pocket1	human		5
80	ORF1ab polyprotein 3943-4140 Non-structural protein 8		-6.65	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	15
81	C type lectin domain family 4 member M		-6.63	Q9H2X3	Pocket1	human	PDB	4
82	ORF1ab polyprotein 1-180 Host translation inhibitor nsp1		-6.5	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
83	Envelope protein	Monomer	-6.29	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	5
84	ORF7a protein		-6.14	QHD43421.1	Pocket1	SARS-CoV-2	Swiss-model	4
85	ORF1ab polyprotein 3860-3942 Non-structural protein 7		-5.65	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	26
86	ORF7a protein		-5.64	P0DTC7	Pocket1	SARS-CoV-2	PDB	22

Note:
^a: Docking score rank with 99 representative structures from 2103 FDA approved drugs, the topper the better (e.g., 3 is better than 20).

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