SARS-CoV-2 3D

Proteinase 3CL-PRO Main protease

UniProt ITasser SWISS Models alphafold D3Targets-2019-nCoV

Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP)

Models/PDB

No model built for protein with good structural coverage represented in PDB

Models/PDB	Model Chains_ID	Selected Templates	Model-Quality (MolProbity)	PDB Coverage	Model Coverage	Sequence Length	Oligomer States	Oligomer Interfaces	Model information
X-RAY_5R7Y Download Pdb file	A	5R7Y; Solved experimentally with good Coverage;	NA	100%	0.00%	306	Homo 2-mer	NA Download interfaces pdf	NA Download model information txt

Models/PDB

Model Chains_ID

Selected Templates

Model-Quality (MolProbity)

PDB Coverage

Model Coverage

Sequence Length

Oligomer States

Oligomer Interfaces

Model information

X-RAY_5R7Y

Download Pdb file

5R7Y; Solved experimentally with good Coverage;

100%

0.00%

306

Homo 2-mer

Download interfaces pdf

Download model information txt

Binding Site Predictions

The fpocket calculation in this table only for structure present in the Model/PDB table above.

fpocket	pocket score	drug score	hydrophobicity score	polarity score
pocket0_protease	33.72	0.64	33.71	7
pocket1_protease	25.31	0.27	12.58	10
pocket2_protease	21.73	0.05	26.2	7
pocket3_protease	15.53	0.11	20.43	6
pocket4_protease	13.7	0.02	12.58	6
pocket5_protease	13.51	0.06	21.13	11
pocket6_protease	11.08	0.01	16.89	5
pocket7_protease	10.33	0.05	33.5	5
pocket8_protease	10.23	0.08	38	6
pocket9_protease	8.47	0.01	8	6

UniProt Viewer

Other PDB Hits

ID	Method	Resolution Å	Chains	Links
7ju7	X-RAY	1.6	A	PDBe RCSB PDB
7jyc	X-RAY	1.79	A	PDBe RCSB PDB
7c2q	X-RAY	1.93	A, B;	PDBe RCSB PDB
7cbt	X-RAY	2.35	A, B;	PDBe RCSB PDB
7c8b	X-RAY	3	A;	PDBe RCSB PDB
7c6s	X-RAY	1.6	A;	PDBe RCSB PDB
7c6u	X-RAY	2	A;	PDBe RCSB PDB
7c2y	X-RAY	1.91	A, B;	PDBe RCSB PDB
7Jun	NEUTRON	2.5	A;	PDBe RCSB PDB
6w79	X-RAY	1.46	A	PDBe RCSB PDB
7jr3	X-RAY	1.55	A	PDBe RCSB PDB
7jr4	X-RAY	1.55	A	PDBe RCSB PDB
6xbi	X-RAY	1.7	A, B, D, E	PDBe RCSB PDB
5rgt	X-RAY	2.22	A	PDBe RCSB PDB
5rf1	X-RAY	1.73	A	PDBe RCSB PDB
5rek	X-RAY	1.74	A	PDBe RCSB PDB
5rfp	X-RAY	2.03	A	PDBe RCSB PDB
5rfg	X-RAY	2.32	A	PDBe RCSB PDB
5rff	X-RAY	1.78	A	PDBe RCSB PDB
5rfq	X-RAY	1.76	A	PDBe RCSB PDB
5rej	X-RAY	1.72	A	PDBe RCSB PDB
5rf0	X-RAY	1.65	A	PDBe RCSB PDB
5rgu	X-RAY	2.11	A	PDBe RCSB PDB
6wqf	X-RAY	2.3	A	PDBe RCSB PDB
6xbh	X-RAY	1.6	A, C	PDBe RCSB PDB
5rh9	X-RAY	1.91	A	PDBe RCSB PDB
5rf2	X-RAY	1.53	A	PDBe RCSB PDB
5reh	X-RAY	1.8	A	PDBe RCSB PDB
5rfs	X-RAY	1.7	A	PDBe RCSB PDB
5rgw	X-RAY	1.43	A	PDBe RCSB PDB
5rfd	X-RAY	1.41	A	PDBe RCSB PDB
5rfe	X-RAY	1.46	A	PDBe RCSB PDB
5rgv	X-RAY	1.82	A	PDBe RCSB PDB
5rfr	X-RAY	1.71	A	PDBe RCSB PDB
5rei	X-RAY	1.82	A	PDBe RCSB PDB
5rf3	X-RAY	1.5	A	PDBe RCSB PDB
5rh8	X-RAY	1.81	A	PDBe RCSB PDB
7buy	X-RAY	1.6	A	PDBe RCSB PDB
5rfa	X-RAY	1.52	A	PDBe RCSB PDB
5rez	X-RAY	1.79	A	PDBe RCSB PDB
5rf7	X-RAY	1.54	A	PDBe RCSB PDB
5rem	X-RAY	1.96	A	PDBe RCSB PDB
5rfv	X-RAY	1.48	A	PDBe RCSB PDB
5rg3	X-RAY	1.58	A	PDBe RCSB PDB
5rgr	X-RAY	1.41	A	PDBe RCSB PDB
5rgs	X-RAY	1.72	A	PDBe RCSB PDB
5rg2	X-RAY	1.63	A	PDBe RCSB PDB
5rfw	X-RAY	1.43	A	PDBe RCSB PDB
5rel	X-RAY	1.62	A	PDBe RCSB PDB
5rf6	X-RAY	1.45	A	PDBe RCSB PDB
6xa4	X-RAY	1.65	A, B	PDBe RCSB PDB
6xch	X-RAY	2.2	A, C	PDBe RCSB PDB
5re8	X-RAY	1.81	A	PDBe RCSB PDB
5rfb	X-RAY	1.48	A	PDBe RCSB PDB
5rey	X-RAY	1.96	A	PDBe RCSB PDB
5rg0	X-RAY	1.72	A	PDBe RCSB PDB
5rgq	X-RAY	2.15	A	PDBe RCSB PDB
5rf4	X-RAY	1.61	A	PDBe RCSB PDB
5ren	X-RAY	2.15	A	PDBe RCSB PDB
5rfu	X-RAY	1.53	A	PDBe RCSB PDB
5rft	X-RAY	1.58	A	PDBe RCSB PDB
5reo	X-RAY	1.88	A	PDBe RCSB PDB
5rf5	X-RAY	1.74	A	PDBe RCSB PDB
5rgp	X-RAY	2.07	A	PDBe RCSB PDB
5rg1	X-RAY	1.65	A	PDBe RCSB PDB
5rex	X-RAY	2.07	A	PDBe RCSB PDB
5rfc	X-RAY	1.4	A	PDBe RCSB PDB
5re9	X-RAY	1.72	A	PDBe RCSB PDB
5rgg	X-RAY	2.26	A	PDBe RCSB PDB
7bro	X-RAY	2	A	PDBe RCSB PDB
6wnp	X-RAY	1.44	A	PDBe RCSB PDB
6m0k	X-RAY	1.5	A	PDBe RCSB PDB
6xkf	X-RAY	1.8	A, B	PDBe RCSB PDB
6xs6	X-RAY	3.7	A, B, C	PDBe RCSB PDB
6wtk	X-RAY	2	A	PDBe RCSB PDB
7c8r	X-RAY	2.3	A	PDBe RCSB PDB
6wtj	X-RAY	1.9	A	PDBe RCSB PDB
6zrt	X-RAY	2.1	A	PDBe RCSB PDB
6lze	X-RAY	1.51	A	PDBe RCSB PDB
6zru	X-RAY	2.1	A	PDBe RCSB PDB
6wtm	X-RAY	1.85	A, B	PDBe RCSB PDB
7jfq	X-RAY	1.55	A	PDBe RCSB PDB
7c8t	X-RAY	2.05	A	PDBe RCSB PDB
7c8u	X-RAY	2.35	A	PDBe RCSB PDB
6m2q	X-RAY	1.7	A	PDBe RCSB PDB
6xhm	X-RAY	1.41	A, B	PDBe RCSB PDB
6xqu	X-RAY	2.2	A	PDBe RCSB PDB
6yvf	X-RAY	1.6	A	PDBe RCSB PDB
6yt8	X-RAY	2.05	A	PDBe RCSB PDB
5r7y	X-RAY	1.65	A	PDBe RCSB PDB
6xqt	X-RAY	2.3	A, B	PDBe RCSB PDB
7brp	X-RAY	1.8	B, A	PDBe RCSB PDB
7brr	X-RAY	1.4	A, B	PDBe RCSB PDB
5r84	X-RAY	1.83	A	PDBe RCSB PDB
5r7z	X-RAY	1.59	A	PDBe RCSB PDB
5r8t	X-RAY	1.27	A	PDBe RCSB PDB
6yb7	X-RAY	1.25	A	PDBe RCSB PDB
6wtt	X-RAY	2.15	A, B, C	PDBe RCSB PDB
6xhu	X-RAY	1.8	A, C	PDBe RCSB PDB
6m03	X-RAY	2	A	PDBe RCSB PDB
6xqs	X-RAY	1.9	A	PDBe RCSB PDB
5r81	X-RAY	1.95	A	PDBe RCSB PDB
6w63	X-RAY	2.1	A	PDBe RCSB PDB
6ynq	X-RAY	1.8	A	PDBe RCSB PDB
7c7p	X-RAY	1.74	A, B	PDBe RCSB PDB
5r80	X-RAY	1.93	A	PDBe RCSB PDB
6xfn	X-RAY	1.7	A, B	PDBe RCSB PDB
6m2n	X-RAY	2.2	A, C, B, D	PDBe RCSB PDB
6yz6	X-RAY	1.7	A, C	PDBe RCSB PDB
5r82	X-RAY	1.31	A	PDBe RCSB PDB
6y84	X-RAY	1.39	A	PDBe RCSB PDB
6lu7	X-RAY	2.16	A, C	PDBe RCSB PDB
5r83	X-RAY	1.58	A	PDBe RCSB PDB
7bqy	X-RAY	1.7	A, C	PDBe RCSB PDB
6xkh	X-RAY	1.28	A	PDBe RCSB PDB
6y2g	X-RAY	2.2	A, B	PDBe RCSB PDB
5rh3	X-RAY	1.69	A	PDBe RCSB PDB
5rhe	X-RAY	1.56	A	PDBe RCSB PDB
5rfn	X-RAY	1.8	A	PDBe RCSB PDB
5re4	X-RAY	1.88	A	PDBe RCSB PDB
5reu	X-RAY	1.69	A	PDBe RCSB PDB
5rgj	X-RAY	1.34	A	PDBe RCSB PDB
5reb	X-RAY	1.68	A	PDBe RCSB PDB
5rf8	X-RAY	1.44	A	PDBe RCSB PDB
5rfy	X-RAY	1.9	A	PDBe RCSB PDB
5rfx	X-RAY	1.55	A	PDBe RCSB PDB
5rf9	X-RAY	1.43	A	PDBe RCSB PDB
5rec	X-RAY	1.73	A	PDBe RCSB PDB
5rgk	X-RAY	1.43	A	PDBe RCSB PDB
5ret	X-RAY	1.68	A	PDBe RCSB PDB
5re5	X-RAY	2.07	A	PDBe RCSB PDB
5rfo	X-RAY	1.83	A	PDBe RCSB PDB
5rhd	X-RAY	1.57	A	PDBe RCSB PDB
5rh2	X-RAY	1.83	A	PDBe RCSB PDB
6y2f	X-RAY	1.95	A	PDBe RCSB PDB
5rh0	X-RAY	1.92	A	PDBe RCSB PDB
5rhf	X-RAY	1.76	A	PDBe RCSB PDB
5rgi	X-RAY	1.57	A	PDBe RCSB PDB
5rfm	X-RAY	2.06	A	PDBe RCSB PDB
5re7	X-RAY	1.79	A	PDBe RCSB PDB
5rev	X-RAY	1.6	A	PDBe RCSB PDB
5rea	X-RAY	1.63	A	PDBe RCSB PDB
5rfz	X-RAY	1.68	A	PDBe RCSB PDB
5rew	X-RAY	1.55	A	PDBe RCSB PDB
5re6	X-RAY	1.87	A	PDBe RCSB PDB
5rfl	X-RAY	1.64	A	PDBe RCSB PDB
5rgh	X-RAY	1.7	A	PDBe RCSB PDB
6y2e	X-RAY	1.75	A	PDBe RCSB PDB
5rh1	X-RAY	1.96	A	PDBe RCSB PDB
6xb0	X-RAY	1.8	A	PDBe RCSB PDB
6xoa	X-RAY	2.1	A, B, C, D	PDBe RCSB PDB
5rhc	X-RAY	1.58	A	PDBe RCSB PDB
5rh5	X-RAY	1.72	A	PDBe RCSB PDB
5red	X-RAY	1.47	A	PDBe RCSB PDB
5rgl	X-RAY	1.76	A	PDBe RCSB PDB
5rfh	X-RAY	1.58	A	PDBe RCSB PDB
5res	X-RAY	1.65	A	PDBe RCSB PDB
5rer	X-RAY	1.88	A	PDBe RCSB PDB
5rfi	X-RAY	1.69	A	PDBe RCSB PDB
5rgm	X-RAY	2.04	A	PDBe RCSB PDB
5ree	X-RAY	1.77	A	PDBe RCSB PDB
5rgz	X-RAY	1.52	A	PDBe RCSB PDB
5rh4	X-RAY	1.34	A	PDBe RCSB PDB
5rhb	X-RAY	1.43	A	PDBe RCSB PDB
6xb1	X-RAY	1.8	A	PDBe RCSB PDB
6xbg	X-RAY	1.45	A, B, C, E	PDBe RCSB PDB
5rh6	X-RAY	1.6	A	PDBe RCSB PDB
5reg	X-RAY	1.67	A	PDBe RCSB PDB
5rgx	X-RAY	1.69	A	PDBe RCSB PDB
5rfk	X-RAY	1.75	A	PDBe RCSB PDB
5rep	X-RAY	1.81	A	PDBe RCSB PDB
5rgo	X-RAY	1.74	A	PDBe RCSB PDB
5rgn	X-RAY	1.86	A	PDBe RCSB PDB
5rfj	X-RAY	1.8	A	PDBe RCSB PDB
5rgy	X-RAY	1.98	A	PDBe RCSB PDB
5ref	X-RAY	1.61	A	PDBe RCSB PDB
5rh7	X-RAY	1.71	A	PDBe RCSB PDB
5rha	X-RAY	1.51	A	PDBe RCSB PDB
6xmk	X-RAY	1.7	A, B	PDBe RCSB PDB
6xb2	X-RAY	2.1	A	PDBe RCSB PDB
6xr3	X-RAY	1.45	A	PDBe RCSB PDB
7com	X-RAY	2.25	A, B	PDBe RCSB PDB
7jox	X-RAY	1.95	A, B;	PDBe RCSB PDB
7joy	X-RAY	2	A, B;	PDBe RCSB PDB
7k6d	X-RAY	1.48	A;	PDBe RCSB PDB
7cwc	X-RAY	2.1	A, B;	PDBe RCSB PDB
7d1o	X-RAY	1.78	A;	PDBe RCSB PDB
7cwb	X-RAY	1.9	A;	PDBe RCSB PDB
7k6e	X-RAY	1.63	A;	PDBe RCSB PDB
7jkv	X-RAY	1.25	A, B;	PDBe RCSB PDB
7jp1	X-RAY	1.8	A;	PDBe RCSB PDB
7k40	X-RAY	1.35	A;	PDBe RCSB PDB
7d3i	X-RAY	2	A;	PDBe RCSB PDB
7k3t	X-RAY	1.2	A;	PDBe RCSB PDB
7d1m	X-RAY	1.35	A, B;	PDBe RCSB PDB
7kfi	X-RAY	1.6	A, B;	PDBe RCSB PDB
7kfj	X-RAY	2.66	A, B;	PDBe RCSB PDB
7aku	X-RAY	2.5	A;	PDBe RCSB PDB
7khp	X-RAY	1.95	A, B;	PDBe RCSB PDB
6z2e	CRYO_EM	1.7	AAA	PDBe RCSB PDB

Predictions of Mutations

pdb_id	mutations	deepddg	maestro	mCSM_ppi	mCSM_Stability	imutant	provean
6y2e	A173F	2.149	-1.838	-0.859	-0.931	Decrease	-2.022
6y2e	A173I	-0.602	-1.899	-0.833	-0.572	Increase	0.28
6y2e	A173L	-0.351	-1.832	-0.833	-0.572	Decrease	-0.653
6y2e	A173Y	1.553	-1.754	-0.83	-1.24	Decrease	-2.022
6y2e	D176C	-2.351	-2.158	-1.117	-1.09	Decrease	-6.619
6y2e	D176F	-2.223	-2.274	-0.686	-1.776	Decrease	-6.766
6y2e	D176I	-1.956	-2.849	-0.342	-0.578	Decrease	-6.752
6y2e	D176L	-2.361	-2.809	-0.342	-0.578	Decrease	-7.389
6y2e	D176M	-2.109	-2.391	0.003	-0.038	Increase	-6.432
6y2e	D176V	-2.621	-2.633	-0.394	-0.822	Increase	-6.739
6y2e	D176W	-2.059	-1.732	-0.871	-2.023	Decrease	-7.735
6y2e	D176Y	-2.654	-1.865	-0.58	-1.666	Increase	-6.566
6y2e	G149C	-3.973	-1.885	-1.913	0.612	Decrease	-8.93
6y2e	G149F	-3.633	-2.068	-1.233	0.402	Decrease	-8.931
6y2e	G149I	-4.045	-2.201	-0.907	1.877	Decrease	-9.917
6y2e	G149L	-4.233	-2.275	-0.907	1.877	Decrease	-9.92
6y2e	G149M	-3.76	-2.01	-1.316	1.302	Decrease	-8.926
6y2e	G149V	-3.649	-2.092	-0.729	1.432	Decrease	-8.923
6y2e	G149Y	-4.567	-1.758	-1.267	0.212	Decrease	-8.931
6y2e	G29C	-3.477	-1.906	-1.893	-1.528	Decrease	-8.962
6y2e	G29I	-3.702	-1.842	-1.664	-0.164	Decrease	-9.958
6y2e	G29M	-3.654	-2.051	-1.559	-0.468	Decrease	-8.962
6y2e	G29V	-3.455	-2.099	-1.499	-0.434	Decrease	-8.962
6y2e	N151F	0.672	-1.97	-1.283	-1.048	Decrease	-4.423
6y2e	N151I	0.366	-1.946	-0.534	-0.466	Decrease	-2.886
6y2e	N151L	0.73	-2.056	-0.534	-0.466	Decrease	-3.619
6y2e	N151M	0.055	-1.83	0.015	-0.202	Decrease	-3.062
6y2e	N151Y	-1.115	-1.768	-1.303	-0.4	Decrease	-3.865
6y2e	N28C	-3.495	-1.751	0.192	-0.159	Decrease	-8.94
6y2e	N28F	-2.812	-2.148	-0.376	0.258	Increase	-8.944
6y2e	N28I	-1.772	-2.088	-0.103	1.145	Increase	-8.942
6y2e	N28L	-2.488	-2.207	-0.103	1.145	Increase	-8.942
6y2e	N28M	-2.572	-2.113	0.059	0.891	Increase	-7.948
6y2e	N28V	-1.877	-1.939	-0.005	1.035	Increase	-8.94
6y2e	N28Y	-3.295	-1.78	-0.134	0.524	Increase	-7.95
6y2e	P39F	-3.399	-2.064	0.442	-1.185	Decrease	-10.954
6y2e	P39I	-3.969	-1.951	0.202	-1.126	Decrease	-9.958
6y2e	P39L	-3.96	-1.985	0.202	-1.126	Decrease	-9.958
6y2e	P39M	-3.755	-1.794	-0.498	-1.219	Decrease	-8.962
6y2e	P39V	-3.427	-1.784	0.218	-1.52	Decrease	-8.962
6y2e	P39Y	-4.618	-1.934	0.569	-1.564	Decrease	-9.958
6y2e	Q127W	-0.556	-1.821	-0.544	-0.391	Decrease	-1.804
6y2e	Q127Y	-2.894	-1.832	-0.246	-0.046	Decrease	-1.375
6y2e	S113F	-1.256	-1.75	-0.081	-1.338	Increase	-4.342
6y2e	S113I	-2.316	-1.879	0.234	-0.858	Increase	-4.108
6y2e	S113V	-1.802	-1.741	0.321	-1.164	Increase	-3.875
6y2e	S113W	-1.711	-1.831	-0.544	-1.415	Increase	-5.104
6y2e	S113Y	-3.932	-1.834	-0.032	-1.128	Increase	-3.875
6y2e	S158F	1.05	-1.748	-0.427	-0.613	Increase	-2.556
6y2e	S158Y	1.852	-1.871	-0.234	-0.453	Decrease	-1.295

Virtual Screening ligands Docking

Docking Structure	pdb	Ligand Name	glide_gscore	MMGBSA_ΔG_Bind	docking_score
NSP-5-6XMK-FDA_1 Download Pdb file	6XMK	MITOXANTRONE	-9.62	-67.72	-9.62
NSP-5-6XMK-FDA_2 Download Pdb file	6XMK	AVANAFIL	-9.46	-53.09	-9.42
NSP-5-6XMK-FDA_3 Download Pdb file	6XMK	PRAVASTATIN	-8.7	-26.02	-8.7
NSP-5-6XMK-FDA_4 Download Pdb file	6XMK	MACIMORELIN	-8.76	-42.79	-8.63
NSP-5-6XMK-FDA_5 Download Pdb file	6XMK	MISOPROSTOL	-8.25	-30.88	-8.25

Protein-Protein Interactions

We have mapped SARS CoV-2 human Protein-Protein Interactions from A SARS-CoV-2 protein interaction map reveals targets for drug repurposing human drug target interacted with SARS CoV-2 are highlighted in black arrow.