D3Targets-2019-nCoV

D3Docking

Job Title:杨梅素对接

Job File:杨梅素分子3D.sdf

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

Molecular Descriptors:Molecular Weight: 318.04
Lipid-Water partition: 1.69
Number of Hydrogen Bond Acceptors: 8
Number of Hydrogen Bond Donors: 6
Number of Rotatable Bonds: 1
Number of Heavy Atoms: 23
Number of Aliphatic Rings of a Molecular: 0
Number of Aromatic Rings of a Molecular: 3
Topological Polar Suface Area: 151.59
Druglikeness: Good

Score:export to excel

Rank	Target Full Name	State	Score	ProteinID	Pocket	Organism	Model Source	Rank^a
1	RNA-dependent RNA polymerase	Only Nsp12 & MD	-11.91	P0DTD1	Pocket3	SARS-CoV-2	Molecular Dynamics	1
2	Dihydroorotate dehydrogenase		-11.84	Q02127	Pocket1	human	PDB	2
3	cGMP-specific 3',5'-cyclic phosphodiesterase		-11.73	O76074	Pocket1	human	PDB	2
4	1-phosphatidylinositol 3-phosphate 5-kinase		-11.48	Q9Y2I7	Pocket2	human	PDB	1
5	RAC-alpha serine/threonine-protein kinase		-11.27	P31749	Pocket1	human	PDB	1
6	Sigma-1 receptor		-11.27	Q99720	Pocket2	human	PDB	1
7	RNA-dependent RNA polymerase	+RNA & +Mg	-11.17	QHD43415.1	Pocket6	SARS-CoV-2	PDB	1
8	Tyrosine-protein kinase ABL2		-11.01	P42684	Pocket1	human	PDB	1
9	Non-structural protein 4		-11.01	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	1
10	Anoctamin-6	Dimer	-10.95	Q4KMQ2	Pocket3	human	Swiss-model	1
11	Anoctamin-6	Monomer	-10.95	Q4KMQ2	Pocket5	human	Swiss-model	1
12	Endoplasmic reticulum chaperone BiP	Monomer	-10.6	P11021	Pocket1	human	PDB	1
13	Spike protein	Closed	-10.54	QHD43416.1	Pocket17	SARS-CoV-2	PDB	1
14	Endoplasmic reticulum chaperone BiP	Dimer	-10.53	P11021	Pocket2	human	PDB	1
15	Mitogen-activated protein kinase 9/c-Jun N-terminal kinase 2		-10.46	P45984	Pocket1	human	Swiss-model	1
16	Spike protein	Open	-10.37	QHD43416.1	Pocket8	SARS-CoV-2	PDB	1
17	Complement Component 5	Monomer	-10.25	P01031	Pocket1	human	PDB	1
18	Complement Component 5	Dimer	-10.23	P01031	Pocket1	human	PDB	1
19	ORF1ab polyprotein 5926-6452 Guanine-N7 methyltransferase		-10.2	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	3
20	Eukaryotic initiation factor 4A-I		-10.2	P60842	Pocket2	human	PDB	1
21	ORF1ab polyprotein 819-2763 Papain-like proteinase	Dimer	-10.05	QHD43415.1	Pocket3	SARS-CoV-2	Swiss-model	2
22	Uridylate-specific endoribonuclease	Dimer	-10.05	QHD43415.1	Pocket3	SARS-CoV-2	PDB	1
23	ORF1ab polyprotein 6453-6798 Uridylate-specific endoribonuclease		-9.99	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	3
24	Non-structural protein 2		-9.98	QHD43415.1	Pocket4	SARS-CoV-2	Robetta	3
25	Bromodomain-containing protein 2	Dimer	-9.98	P25440	Pocket1	human	PDB	1
26	Uridylate-specific endoribonuclease	Monomer	-9.93	QHD43415.1	Pocket1	SARS-CoV-2	PDB	1
27	Caveolin-2		-9.92	P51636	Pocket1	human	Robetta	1
28	ORF1ab polyprotein 6799-7096 2'-O-methyltransferase		-9.92	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
29	2'-O-Methyltransferase		-9.87	P0DTD1	Pocket1	SARS-CoV-2	PDB	1
30	ORF1ab 5325-5925 Helicase	Dimer	-9.83	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
31	Angiotensin converting enzyme 2		-9.83	P59594	Pocket1	human	PDB	2
32	Mitogen-activated protein kinase 8/c-Jun N-terminal kinase 1		-9.79	P45983	Pocket1	human	Swiss-model	1
33	ADP ribose phosphatase	Monomer	-9.77	QHD43415.1	Pocket1	SARS-CoV-2	PDB	3
34	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase		-9.76	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
35	Nucleocapsid phosphoprotein	N terminal	-9.76	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	1
36	ORF1ab polyprotein 4393-5324 RNA-dependent RNA polymerase	+Mg	-9.76	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
37	ADP ribose phosphatase	Dimer	-9.76	QHD43415.1	Pocket2	SARS-CoV-2	PDB	2
38	RAC-beta serine/threonine-protein kinase		-9.71	P31751	Pocket1	human	PDB	2
39	Elongation factor 1-alpha 1		-9.68	P68104	Pocket1	human	PDB	1
40	Mitogen-activated protein kinase 10/c-Jun N-terminal kinase 3		-9.64	P53779	Pocket1	human	PDB	2
41	Transmembrane protease serine 2		-9.64	O15393	Pocket4	human	Robetta	1
42	Heterogeneous nuclear ribonucleoprotein A1		-9.53	P09651	Pocket1	human	PDB	2
43	Papain-like proteinase	Trimer	-9.53	QHD43415.1	Pocket3	SARS-CoV-2	PDB	2
44	ORF1ab polyprotein 3264-3569 3C-like proteinase	Dimer	-9.52	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	1
45	AP2-associated protein kinase 1		-9.48	Q2M2I8	Pocket1	human	PDB	1
46	Complement Component 3		-9.48	P01024	Pocket3	human	PDB	1
47	Glycogen synthase kinase-3 beta		-9.48	P49841	Pocket8	human	PDB	1
48	Spike protein	Closed	-9.42	QHD43416.1	Pocket1	SARS-CoV-2	Swiss-model	2
49	Nucleocapsid phosphoprotein	N terminal & Tetramer	-9.38	QHD43423.2	Pocket2	SARS-CoV-2	PDB	2
50	Nucleocapsid phosphoprotein	C terminal & Dimer	-9.29	P0DTC9	Pocket1	SARS-CoV-2	PDB	1
51	Furin		-9.28	P09958	Pocket1	human	PDB	1
52	3C-like proteinase	Dimer	-9.25	QHD43415.1	Pocket1	SARS-CoV-2	PDB	2
53	Citrate lyase subunit beta-like protein, mitochondrial		-9.23	Q8N0X4	Pocket2	human	PDB	1
54	Nonstructural protein NS8	Dimer	-9.23	A0A6C0N6C6	Pocket1	SARS-CoV-2	PDB	2
55	ORF1ab polyprotein 5325-5925 Helicase	Monomer	-9.2	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	4
56	Spike protein	Open	-9.14	QHD43416.1	Pocket1	SARS-CoV-2	Swiss-model	1
57	3C-like proteinase	MD	-9.12	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	1
58	ORF1ab polyprotein 3264-3569 3C-like proteinase	Monomer	-8.98	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
59	Heat shock protein 90		-8.97	P07900	Pocket3	human	PDB	2
60	3C-like proteinase	MD	-8.94	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	1
61	Disintegrin and metalloproteinase domain-containing protein 17	+Zn	-8.94	P78536	Pocket1	human		2
62	3C-like proteinase	MD	-8.88	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
63	Spike protein S2 subunit		-8.87	/	Pocket1	SARS-CoV-2	PDB	2
64	RNA-dependent RNA polymerase		-8.81	QHD43415.1	Pocket2	SARS-CoV-2	PDB	1
65	Disintegrin and metalloproteinase domain-containing protein 17		-8.77	P78536	Pocket1	human	Swiss-model	3
66	ORF1ab polyprotein 819-2763 Papain-like proteinase	Monomer	-8.76	QHD43415.1	Pocket4	SARS-CoV-2	Swiss-model	3
67	SARS-COV-2 chimeric receptor-binding domain+Angiotensin converting enzyme 2		-8.75	/	Pocket1	human	PDB	2
68	Bromodomain-containing protein 2	Monomer	-8.75	P25440	Pocket1	human	PDB	1
69	Nucleocapsid phosphoprotein	C terminal & Monomer	-8.74	P0DTC9	Pocket1	SARS-CoV-2	PDB	4
70	Plasminogen activator inhibitor 1	Monomer	-8.7	P05121	Pocket3	human	PDB	1
71	Cathepsin L		-8.66	P07711	Pocket2	human	PDB	1
72	Cyclophilin A		-8.65	P62937	Pocket1	human	PDB	3
73	3C-like proteinase	Monomer	-8.58	QHD43415.1	Pocket2	SARS-CoV-2	PDB	2
74	3C-like proteinase	MD	-8.54	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
75	Nucleocapsid phosphoprotein	N terminal & Monomer	-8.53	QHD43423.2	Pocket1	SARS-CoV-2	PDB	1
76	Calnexin		-8.53	P27824	Pocket4	human	Swiss-model	1
77	Non-structural protein 7 + Non-structural protein 8	Complex	-8.44	P0DTC1	Pocket3	SARS-CoV-2	PDB	1
78	Envelope protein	Pentamer	-8.39	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	6
79	Tyrosine-protein kinase receptor UFO		-8.35	P30530	Pocket1	human	PDB	1
80	RAC-gamma serine/threonine-protein kinase		-8.32	Q9Y243	Pocket1	human	PDB	1
81	Nonstructural protein NS8	Monomer	-8.28	A0A6C0N6C6	Pocket1	SARS-CoV-2	PDB	1
82	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Dimer	-8.25	QHD43415.1	Pocket3	SARS-CoV-2	Swiss-model	1
83	Calnexin	+Ca	-8.23	P27823	Pocket4	human		1
84	Basigin		-8.14	P35613	Pocket2	human	PDB	1
85	ORF1ab polyprotein 4254-4392 Non-structural protein 10		-8.11	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	1
86	Cathepsin L		-8.1	P07711	Pocket4	human	PDB	1
87	ORF1ab polyprotein 4141-4253 Non-structural protein 9	Monomer	-7.94	QHD43415.1	Pocket2	SARS-CoV-2	Swiss-model	3
88	Non-structural protein 6		-7.9	QHD43415.1	Pocket1	SARS-CoV-2	Robetta	7
89	Papain-like protease	Monomer	-7.86	QHD43415.1	Pocket7	SARS-CoV-2	PDB	1
90	Nucleocapsid phosphoprotein	C terminal	-7.82	QHD43423.2	Pocket1	SARS-CoV-2	Swiss-model	7
91	C type lectin domain family 4 member M		-7.8	Q9H2X3	Pocket2	human	PDB	1
92	Envelope protein	Pentamer	-7.7	P0DTC4	Pocket1	SARS-CoV-2	PDB	22
93	Spike protein-heptad repeat 1		-7.64	QHD43416.1	Pocket1	SARS-CoV-2	Swiss-model	1
94	Guanylate kinase		-7.6	Q16774	Pocket1	human	PDB	1
95	Non-structural protein 9	Dimer	-7.6	QHD43415.1	Pocket4	SARS-CoV-2	PDB	1
96	Non-structural protein 10		-7.55	P0DTC1	Pocket1	SARS-CoV-2	PDB	6
97	ORF1ab polyprotein 3943-4140 Non-structural protein 8		-7.48	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	4
98	ORF7a protein		-7.36	P0DTC7	Pocket1	SARS-CoV-2	PDB	1
99	ORF1ab polyprotein 1-180 Host translation inhibitor nsp1		-7.18	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
100	ORF1ab polyprotein 3860-3942 Non-structural protein 7		-7.17	QHD43415.1	Pocket1	SARS-CoV-2	Swiss-model	2
101	Non-structural protein 9	Monomer	-6.94	QHD43415.1	Pocket1	SARS-CoV-2	PDB	6
102	Envelope protein	Monomer	-6.43	QHD43418.1	Pocket1	SARS-CoV-2	Swiss-model	4
103	ORF7a protein		-6.31	QHD43421.1	Pocket1	SARS-CoV-2	Swiss-model	3

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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