D3Targets-2019-nCoV

D3Docking

Job Title:title_200527203704

Job File:Remdesivir-meta.sdf

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

Molecular Descriptors:Molecular Weight: 526.97
Lipid-Water partition: -4.03
Number of Hydrogen Bond Acceptors: 18
Number of Hydrogen Bond Donors: 3
Number of Rotatable Bonds: 8
Number of Heavy Atoms: 33
Number of Aliphatic Rings of a Molecular: 1
Number of Aromatic Rings of a Molecular: 2
Topological Polar Suface Area: 300.83
Druglikeness: Maybe bad

Score:export to excel

Rank	Target Full Name	State	Score	ProteinID	Pocket	Organism	Model Source	Rank^a
1	RNA-dependent RNA polymerase	+RNA & +Mg	-12.95	QHD43415.1	Pocket1	SARS-CoV-2	PDB	1
2	Eukaryotic initiation factor 4A-I		-11.88	P60842	Pocket2	human	PDB	1
3	Dihydroorotate dehydrogenase		-11.54	Q02127	Pocket1	human	PDB	2
4	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase	+Mg	-11.37	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
5	cGMP-specific 3',5'-cyclic phosphodiesterase		-10.35	O76074	Pocket1	human	PDB	9
6	Spike protein	Open	-10.28	QHD43416.1	Pocket8	SARS-CoV-2	PDB	1
7	ADP ribose phosphatase	Dimer	-10.15	QHD43415.1	Pocket2	SARS-CoV-2	PDB	2
8	ADP ribose phosphatase	Monomer	-10.1	QHD43415.1	Pocket1	SARS-CoV-2	PDB	2
9	Mitogen-activated protein kinase 10/c-Jun N-terminal kinase 3		-9.98	P53779	Pocket1	human	PDB	1
10	RNA-dependent RNA polymerase		-9.97	QHD43415.1	Pocket4	SARS-CoV-2	PDB	1
11	ORF1ab polyprotein 6453-6798 Uridylate-specific endoribonuclease		-9.84	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
12	ORF1ab polyprotein 5926-6452 Guanine-N7 methyltransferase		-9.67	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	6
13	Spike protein	Closed	-9.44	QHD43416.1	Pocket10	SARS-CoV-2	PDB	1
14	RAC-alpha serine/threonine-protein kinase		-9.4	P31749	Pocket1	human	PDB	11
15	3C-like proteinase	MD	-9.39	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	1
16	ORF1ab polyprotein 819-2763 Papain-like proteinase	Dimer	-9.36	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	5
17	Complement Component 5	Monomer	-9.32	P01031	Pocket1	human	PDB	4
18	Spike protein S2 subunit		-9.09	/	Pocket1	SARS-CoV-2	PDB	1
19	Non-structural protein 2		-9.06	QHD43415.1	Pocket3	SARS-CoV-2	Robetta	4
20	Complement Component 5	Dimer	-8.91	P01031	Pocket1	human	PDB	5
21	Furin		-8.9	P09958	Pocket1	human	PDB	1
22	Papain-like proteinase	Trimer	-8.85	QHD43415.1	Pocket1	SARS-CoV-2	PDB	4
23	3C-like proteinase	Dimer	-8.84	QHD43415.1	Pocket2	SARS-CoV-2	PDB	3
24	3C-like proteinase	MD	-8.83	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
25	Complement Component 3		-8.81	P01024	Pocket1	human	PDB	2
26	ORF1ab polyprotein 3264-3569 3C-like proteinase	Dimer	-8.71	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
27	Caveolin-2		-8.7	P51636	Pocket1	human	Robetta	14
28	Mitogen-activated protein kinase 9/c-Jun N-terminal kinase 2		-8.69	P45984	Pocket1	human	Swiss-model	11
29	Nucleocapsid phosphoprotein	N terminal & Tetramer	-8.64	QHD43423.2	Pocket2	SARS-CoV-2	PDB	2
30	Non-structural protein 4		-8.63	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	9
31	Transmembrane protease serine 2		-8.58	O15393	Pocket1	human	Robetta	3
32	Heterogeneous nuclear ribonucleoprotein A1		-8.53	P09651	Pocket1	human	PDB	7
33	ORF1ab polyprotein 5325-5925 Helicase	Monomer	-8.51	QHD43415.1	Pocket3	SARS-CoV-2	Swiss-model	1
34	Spike protein	Open	-8.49	QHD43416.1	Pocket4	SARS-CoV-2	Swiss-model	5
35	Uridylate-specific endoribonuclease	Dimer	-8.48	QHD43415.1	Pocket2	SARS-CoV-2	PDB	8
36	ORF1ab 5325-5925 Helicase	Dimer	-8.47	QHD43415.1	Pocket8	SARS-CoV-2	Swiss-model	1
37	3C-like proteinase	MD	-8.47	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	3
38	ORF1ab polyprotein 6799-7096 2'-O-methyltransferase		-8.46	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	3
39	SARS-COV-2 chimeric receptor-binding domain+Angiotensin converting enzyme 2		-8.42	/	Pocket1	human	PDB	5
40	3C-like proteinase	Monomer	-8.36	QHD43415.1	Pocket1	SARS-CoV-2	PDB	1
41	Disintegrin and metalloproteinase domain-containing protein 17		-8.28	P78536	Pocket1	human	Swiss-model	4
42	Glycogen synthase kinase-3 beta		-8.25	P49841	Pocket1	human	PDB	9
43	Angiotensin converting enzyme 2		-8.24	P59594	Pocket1	human	PDB	8
44	Disintegrin and metalloproteinase domain-containing protein 17	+Zn	-8.19	P78536	Pocket1	human		6
45	Nucleocapsid phosphoprotein	N terminal	-8.19	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	16
46	ORF1ab polyprotein 3264-3569 3C-like proteinase	Monomer	-8.1	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
47	Papain-like protease	Monomer	-8.06	QHD43415.1	Pocket5	SARS-CoV-2	PDB	2
48	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase		-8.01	QHD43415.1	Pocket3	SARS-CoV-2	Swiss-model	8
49	AP2-associated protein kinase 1		-7.96	Q2M2I8	Pocket5	human	PDB	2
50	Mitogen-activated protein kinase 8/c-Jun N-terminal kinase 1		-7.95	P45983	Pocket3	human	Swiss-model	11
51	Spike protein	Closed	-7.91	QHD43416.1	Pocket3	SARS-CoV-2	Swiss-model	1
52	ORF1ab polyprotein 819-2763 Papain-like proteinase	Monomer	-7.91	QHD43415.1	Pocket6	SARS-CoV-2	Swiss-model	1
53	Non-structural protein 6		-7.86	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	7
54	Tyrosine-protein kinase ABL2		-7.79	P42684	Pocket1	human	PDB	25
55	RAC-beta serine/threonine-protein kinase		-7.77	P31751	Pocket4	human	PDB	2
56	C type lectin domain family 4 member M		-7.61	Q9H2X3	Pocket1	human	PDB	2
57	Uridylate-specific endoribonuclease	Monomer	-7.59	QHD43415.1	Pocket1	SARS-CoV-2	PDB	14
58	3C-like proteinase	MD	-7.55	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
59	Calnexin		-7.5	P27824	Pocket4	human	Swiss-model	3
60	Cyclophilin A		-7.35	P62937	Pocket2	human	PDB	1
61	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Dimer	-7.2	QHD43415.1	Pocket3	SARS-CoV-2	Swiss-model	1
62	Non-structural protein 9	Dimer	-7.18	QHD43415.1	Pocket4	SARS-CoV-2	PDB	1
63	Nucleocapsid phosphoprotein	N terminal & Monomer	-7.1	QHD43423.2	Pocket2	SARS-CoV-2	PDB	1
64	Envelope protein	Pentamer	-7.06	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	25
65	Non-structural protein 9	Monomer	-6.96	QHD43415.1	Pocket3	SARS-CoV-2	PDB	1
66	Cathepsin L		-6.92	P07711	Pocket1	human	PDB	8
67	ORF1ab polyprotein 4254-4392 Non-structural protein 10		-6.91	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	2
68	ORF1ab polyprotein 1-180 Host translation inhibitor nsp1		-6.81	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
69	Spike protein-heptad repeat 1		-6.69	QHD43416.1	Pocket1	SARS-CoV-2	Swiss-model	9
70	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Monomer	-6.68	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
71	Calnexin	+Ca	-6.59	P27823	Pocket2	human		3
72	Nucleocapsid phosphoprotein	C terminal	-6.52	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	29
73	Envelope protein	Monomer	-6.44	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	4
74	RAC-gamma serine/threonine-protein kinase		-6.33	Q9Y243	Pocket1	human	PDB	18
75	ORF7a protein		-5.97	QHD43421.1	Pocket1	SARS-CoV-2	Swiss-model	6
76	ORF1ab polyprotein 3943-4140 Non-structural protein 8		-5.76	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	30
77	ORF1ab polyprotein 3860-3942 Non-structural protein 7		-5.13	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	38

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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