D3Targets-2019-nCoV

D3Docking

Job Title:md1

Job File:ritonavir.sdf

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	1-phosphatidylinositol 3-phosphate 5-kinase		-11.44	Q9Y2I7	Pocket2	human	PDB	1
2	RAC-alpha serine/threonine-protein kinase		-10.77	P31749	Pocket1	human	PDB	3
3	3C-like proteinase	Dimer	-9.85	QHD43415.1	Pocket2	SARS-CoV-2	PDB	1
4	Caveolin-2		-9.62	P51636	Pocket1	human	Robetta	2
5	Anoctamin-6	Monomer	-9.61	Q4KMQ2	Pocket2	human	Swiss-model	2
6	ORF1ab polyprotein 5926-6452 Guanine-N7 methyltransferase		-9.6	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	6
7	Disintegrin and metalloproteinase domain-containing protein 17	+Zn	-9.51	P78536	Pocket1	human		1
8	Mitogen-activated protein kinase 10/c-Jun N-terminal kinase 3		-9.49	P53779	Pocket1	human	PDB	3
9	Disintegrin and metalloproteinase domain-containing protein 17		-9.47	P78536	Pocket1	human	Swiss-model	1
10	Spike protein	Open	-9.46	QHD43416.1	Pocket2	SARS-CoV-2	PDB	4
11	Elongation factor 1-alpha 1		-9.34	P68104	Pocket1	human	PDB	2
12	ADP ribose phosphatase	Dimer	-9.31	QHD43415.1	Pocket3	SARS-CoV-2	PDB	4
13	Complement Component 5	Dimer	-9.28	P01031	Pocket1	human	PDB	4
14	ORF1ab polyprotein 6453-6798 Uridylate-specific endoribonuclease		-9.27	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
15	Eukaryotic initiation factor 4A-I		-9.26	P60842	Pocket2	human	PDB	5
16	Envelope protein	Pentamer	-9.25	P0DTC4	Pocket1	SARS-CoV-2	PDB	6
17	Complement Component 5	Monomer	-9.25	P01031	Pocket1	human	PDB	4
18	Non-structural protein 4		-9.23	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	6
19	Spike protein	Closed	-9.2	QHD43416.1	Pocket2	SARS-CoV-2	PDB	3
20	Papain-like proteinase	Trimer	-9.17	QHD43415.1	Pocket1	SARS-CoV-2	PDB	2
21	Angiotensin converting enzyme 2		-9.12	P59594	Pocket1	human	PDB	3
22	ORF1ab polyprotein 819-2763 Papain-like proteinase	Dimer	-9.11	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	6
23	ORF1ab polyprotein 3264-3569 3C-like proteinase	Dimer	-9.11	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	2
24	ADP ribose phosphatase	Monomer	-9.08	QHD43415.1	Pocket1	SARS-CoV-2	PDB	6
25	Glycogen synthase kinase-3 beta		-9.01	P49841	Pocket1	human	PDB	4
26	Anoctamin-6	Dimer	-8.97	Q4KMQ2	Pocket1	human	Swiss-model	7
27	RNA-dependent RNA polymerase	+RNA & +Mg	-8.93	QHD43415.1	Pocket1	SARS-CoV-2	PDB	4
28	Nucleocapsid phosphoprotein	N terminal & Tetramer	-8.92	QHD43423.2	Pocket1	SARS-CoV-2	PDB	4
29	SARS-COV-2 chimeric receptor-binding domain+Angiotensin converting enzyme 2		-8.88	/	Pocket1	human	PDB	2
30	Tyrosine-protein kinase ABL2		-8.82	P42684	Pocket1	human	PDB	6
31	Complement Component 3		-8.79	P01024	Pocket1	human	PDB	2
32	Mitogen-activated protein kinase 8/c-Jun N-terminal kinase 1		-8.75	P45983	Pocket1	human	Swiss-model	8
33	Envelope protein	Pentamer	-8.72	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	5
34	Non-structural protein 7 + Non-structural protein 8	Complex	-8.71	P0DTC1	Pocket1	SARS-CoV-2	PDB	2
35	Nucleocapsid phosphoprotein	C terminal & Monomer	-8.66	P0DTC9	Pocket1	SARS-CoV-2	PDB	5
36	RNA-dependent RNA polymerase	Only Nsp12 & MD	-8.64	P0DTD1	Pocket2	SARS-CoV-2	Molecular Dynamics	2
37	Non-structural protein 2		-8.63	QHD43415.1	Pocket2	SARS-CoV-2	Robetta	2
38	Uridylate-specific endoribonuclease	Dimer	-8.61	QHD43415.1	Pocket3	SARS-CoV-2	PDB	4
39	Heterogeneous nuclear ribonucleoprotein A1		-8.59	P09651	Pocket1	human	PDB	7
40	Dihydroorotate dehydrogenase		-8.58	Q02127	Pocket1	human	PDB	28
41	ORF1ab 5325-5925 Helicase	Dimer	-8.54	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
42	Nucleocapsid phosphoprotein	N terminal	-8.53	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	12
43	Mitogen-activated protein kinase 9/c-Jun N-terminal kinase 2		-8.46	P45984	Pocket1	human	Swiss-model	13
44	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase	+Mg	-8.39	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	3
45	ORF1ab polyprotein 5325-5925 Helicase	Monomer	-8.33	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	10
46	RNA-dependent RNA polymerase		-8.31	QHD43415.1	Pocket2	SARS-CoV-2	PDB	2
47	Heat shock protein 90		-8.3	P07900	Pocket3	human	PDB	3
48	Nucleocapsid phosphoprotein	C terminal	-8.24	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	6
49	Transmembrane protease serine 2		-8.23	O15393	Pocket1	human	Robetta	6
50	Spike protein	Open	-8.21	QHD43416.1	Pocket4	SARS-CoV-2	Swiss-model	10
51	RAC-beta serine/threonine-protein kinase		-8.16	P31751	Pocket1	human	PDB	9
52	Furin		-8.14	P09958	Pocket1	human	PDB	7
53	Spike protein	Closed	-8.13	QHD43416.1	Pocket5	SARS-CoV-2	Swiss-model	3
54	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase		-8.13	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	3
55	ORF1ab polyprotein 3264-3569 3C-like proteinase	Monomer	-8.11	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
56	ORF1ab polyprotein 819-2763 Papain-like proteinase	Monomer	-8.03	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	10
57	Uridylate-specific endoribonuclease	Monomer	-7.98	QHD43415.1	Pocket1	SARS-CoV-2	PDB	11
58	Non-structural protein 6		-7.92	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	7
59	3C-like proteinase	MD	-7.84	QHD43415.1	Pocket4	SARS-CoV-2	Swiss-model	2
60	Nonstructural protein NS8	Dimer	-7.74	A0A6C0N6C6	Pocket1	SARS-CoV-2	PDB	13
61	Tyrosine-protein kinase receptor UFO		-7.74	P30530	Pocket1	human	PDB	7
62	AP2-associated protein kinase 1		-7.73	Q2M2I8	Pocket5	human	PDB	2
63	Spike protein-heptad repeat 1		-7.7	QHD43416.1	Pocket3	SARS-CoV-2	Swiss-model	4
64	ORF1ab polyprotein 6799-7096 2'-O-methyltransferase		-7.7	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	6
65	Nucleocapsid phosphoprotein	C terminal & Dimer	-7.64	P0DTC9	Pocket2	SARS-CoV-2	PDB	4
66	Non-structural protein 10		-7.57	P0DTC1	Pocket1	SARS-CoV-2	PDB	5
67	3C-like proteinase	Monomer	-7.56	QHD43415.1	Pocket2	SARS-CoV-2	PDB	6
68	Guanylate kinase		-7.52	Q16774	Pocket1	human	PDB	2
69	3C-like proteinase	MD	-7.52	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	12
70	2'-O-Methyltransferase		-7.51	P0DTD1	Pocket1	SARS-CoV-2	PDB	10
71	Cathepsin L		-7.5	P07711	Pocket2	human	PDB	4
72	cGMP-specific 3',5'-cyclic phosphodiesterase		-7.49	O76074	Pocket1	human	PDB	46
73	Spike protein S2 subunit		-7.48	/	Pocket1	SARS-CoV-2	PDB	9
74	3C-like proteinase	MD	-7.44	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	5
75	Non-structural protein 9	Dimer	-7.42	QHD43415.1	Pocket2	SARS-CoV-2	PDB	4
76	Sigma-1 receptor		-7.28	Q99720	Pocket1	human	PDB	5
77	Non-structural protein 9	Monomer	-7.21	QHD43415.1	Pocket1	SARS-CoV-2	PDB	3
78	Papain-like protease	Monomer	-7.12	QHD43415.1	Pocket2	SARS-CoV-2	PDB	3
79	Plasminogen activator inhibitor 1	Monomer	-7.12	P05121	Pocket2	human	PDB	8
80	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Dimer	-7.09	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	5
81	3C-like proteinase	MD	-7.06	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	12
82	Nonstructural protein NS8	Monomer	-7.02	A0A6C0N6C6	Pocket2	SARS-CoV-2	PDB	18
83	ORF1ab polyprotein 4254-4392 Non-structural protein 10		-6.94	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	10
84	RAC-gamma serine/threonine-protein kinase		-6.82	Q9Y243	Pocket4	human	PDB	1
85	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Monomer	-6.77	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	14
86	Calnexin		-6.72	P27824	Pocket2	human	Swiss-model	2
87	Cyclophilin A		-6.7	P62937	Pocket1	human	PDB	17
88	Calnexin	+Ca	-6.65	P27823	Pocket5	human		4
89	Nucleocapsid phosphoprotein	N terminal & Monomer	-6.56	QHD43423.2	Pocket1	SARS-CoV-2	PDB	9
90	C type lectin domain family 4 member M		-6.53	Q9H2X3	Pocket1	human	PDB	4
91	ORF1ab polyprotein 1-180 Host translation inhibitor nsp1		-6.39	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	6
92	Envelope protein	Monomer	-6.37	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	4
93	ORF1ab polyprotein 3943-4140 Non-structural protein 8		-6.25	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	22
94	Basigin		-6.24	P35613	Pocket2	human	PDB	7
95	ORF1ab polyprotein 3860-3942 Non-structural protein 7		-5.55	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	28
96	ORF7a protein		-4.8	QHD43421.1	Pocket1	SARS-CoV-2	Swiss-model	44
97	ORF7a protein		-4.64	P0DTC7	Pocket1	SARS-CoV-2	PDB	57

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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