SARS-CoV-2 3D

RNA polymerase nsp12

UniProt ITasser SWISS Models alphafold D3Targets-2019-nCoV

Responsible for replication and transcription of the viral RNA genome

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
nsp12 Download Pdb file	A	6M5I; 6YYT; 7C2K; 6XEZ;	2.78	91.40%	100%	932	Hetero 4-mer	nsp12 Download interfaces pdf	nsp12 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

nsp12

Download Pdb file

6M5I; 6YYT; 7C2K; 6XEZ;

2.78

91.40%

100%

932

Hetero 4-mer

nsp12

Download interfaces pdf

nsp12

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_nsp12	31.53	0.04	-1	11
pocket1_nsp12	29.69	0.05	20.92	5
pocket2_nsp12	29.66	0.02	14.91	8

UniProt Viewer

Other PDB Hits

ID	Method	Resolution Å	Chains	Links
7cxm	CRYO_EM	2.9	A	PDBe RCSB PDB
7cxn	CRYO_EM	3.84	A	PDBe RCSB PDB
7ctt	CRYO_EM	3.2	A, B, D, C, Q, T;	PDBe RCSB PDB
7bv2	X-RAY	2.5	A	PDBe RCSB PDB
6wkq	X-RAY	1.9	A,B	PDBe RCSB PDB
6xqb	X-RAY	3.4	A,B,C,D	PDBe RCSB PDB
6xez	CRYO_EM	3.5	A,B,C,D,E,F	PDBe RCSB PDB
7bw4	CRYO_EM	3.7	A,B,C,D	PDBe RCSB PDB
6m71	CRYO_EM	2.9	A,C,D,B	PDBe RCSB PDB
6yyt	CRYO_EM	2.9	A,B,C,D,P,Q,T,U	PDBe RCSB PDB
7bv1	CRYO_EM	2.8	A,B,C,D	PDBe RCSB PDB
7bzf	CRYO_EM	3.26	A,B,C,D,F,G	PDBe RCSB PDB
7btf	CRYO_EM	2.95	A	PDBe RCSB PDB
7aap	CRYO_EM	2.6	A, B, C;	PDBe RCSB PDB

Predictions of Mutations

pdb_id	mutations	deepddg	maestro	mCSM_ppi	mCSM_Stability	imutant	provean
7btf	A685W	0.162	-0.368324	0.988	-1.036	Decrease	-6.417
7btf	A685F	0.227	-0.35192	0.882	-0.859	Decrease	-5.5
7btf	A685Y	-0.142	-0.324089	0.918	-0.657	Decrease	-5.5
7btf	K508R	-0.348	-0.317922	-0.392	-0.505	Decrease	-3
7btf	D418K	-0.062	-0.299498	0.513	-0.131	Decrease	-3.881
7btf	A685M	0.044	-0.298125	0.421	-0.371	Decrease	-4.583
7btf	D418R	-0.289	-0.295841	0.362	0.1	Decrease	-4.855
7btf	D418E	0.068	-0.27992	-0.222	-0.549	Decrease	-1.845
7btf	K508W	-0.917	-0.27185	-1.687	-0.618	Decrease	-8
7btf	K574W	-0.437	-0.270264	-0.037	-0.414	Increase	-8
7btf	A685L	0.31	-0.267376	0.058	-0.251	Decrease	-4.583
7btf	D418Y	-0.551	-0.261341	-0.003	0.246	Decrease	-6.315
7btf	D418F	-0.116	-0.240411	-0.013	0.004	Decrease	-6.674
7btf	D60W	-0.619	-0.238167	-0.287	-0.496	Decrease	-0.752
7btf	S364R	-0.605	-0.236364	0.5	-0.159	Increase	-3.532
7btf	D418Q	-0.108	-0.235118	-0.52	-0.469	Decrease	-3.466
7btf	A685R	-0.158	-0.228823	-0.169	-0.228	Decrease	-4.583
7btf	K47F	-0.622	-0.225895	-1.655	-0.571	Increase	-6.716
7btf	D418W	-0.181	-0.223788	-0.22	0.197	Decrease	-7.384
7btf	A685Q	-0.304	-0.221254	0.373	-0.447	Decrease	-4.583
7btf	D60Y	-1.077	-0.220573	0.013	-0.329	Decrease	-1.063
7btf	K574R	-0.199	-0.212348	-0.371	-0.378	Increase	-3
7btf	E58W	-1.525	-0.207546	-1.411	-2.444	Decrease	-3.89
7btf	D418M	-0.197	-0.202036	0.997	0.703	Decrease	-6.235
7btf	K47Y	-0.816	-0.197101	-1.691	-0.185	Increase	-5.876
7btf	D418H	-0.022	-0.191458	0.873	-0.118	Decrease	-4.385
7btf	V338Q	-0.859	-0.186484	-0.62	-0.553	Decrease	-5.55
7btf	K47C	-1.105	-0.184035	-0.939	-0.918	Increase	-6.716
7btf	D481R	-0.313	-0.179799	0.645	-0.034	Decrease	-5.277
7btf	V338E	-1.064	-0.179129	-0.691	-0.16	Decrease	-5.55
7btf	V338W	-0.227	-0.177382	-0.191	-0.71	Decrease	-6.265
7btf	A526R	-0.582	-0.176121	-1.876	-0.906	Decrease	-3.9
7btf	K508Y	-0.803	-0.173617	-1.6	-0.344	Increase	-7
7btf	K508F	-0.775	-0.172882	-1.493	-0.655	Increase	-8
7btf	K47W	-0.457	-0.170802	-1.725	-0.44	Decrease	-6.716
7btf	A685H	-0.319	-0.170545	0.842	-0.551	Decrease	-5.5
7btf	A699R	-3.443	-0.168488	-2.427	-1.646	Decrease	-4.24
7btf	A685P	0.272	-0.168395	0.009	-0.262	Increase	-4.583
7btf	D418L	-0.039	-0.167399	0.424	0.413	Decrease	-7.177
7btf	A685N	-0.281	-0.165876	0.203	-0.238	Decrease	-5.5
7btf	Y455W	-0.892	-0.163346	-0.945	-0.658	Decrease	-4.741
7btf	D418N	-0.319	-0.162283	-1.117	-0.615	Decrease	-2.503
7btf	D418I	-0.022	-0.15879	0.424	0.413	Decrease	-6.674
7btf	A685K	-0.105	-0.158495	0.273	-0.596	Decrease	-4.583
7btf	A685I	0.212	-0.158008	0.058	-0.251	Decrease	-4.583
7btf	K47M	-0.538	-0.15668	-0.996	-0.347	Increase	-5.037
7btf	S236R	-3.295	-0.153879	-0.229	-0.559	Decrease	-4.242
7btf	A376R	-3.631	-0.151166	-2.119	-1.603	Decrease	-3.517
7btf	K47L	-0.313	-0.147276	-1.491	-0.041	Increase	-5.876
7btf	D208W	-1.203	-0.145962	-0.362	-0.68	Decrease	-8.417

Virtual Screening ligands Docking

Docking Structure	pdb	Ligand Name	glide_gscore	MMGBSA_ΔG_Bind	docking_score
NSP-12-7C2K-FDA_1 Download Pdb file	7C2K	MITOXANTRONE	-13.44	-89.95	-13.44
NSP-12-7C2K-FDA_2 Download Pdb file	7C2K	MINOCYCLINE	-10.72	-56.72	-10.61
NSP-12-7C2K-FDA_3 Download Pdb file	7C2K	AMODIAQUINE	-10.4	-54.65	-9.81
NSP-12-7C2K-FDA_4 Download Pdb file	7C2K	MACIMORELIN	-10.17	-49.22	-10.05
NSP-12-7C2K-FDA_5 Download Pdb file	7C2K	INDACATEROL	-10.17	-26.43	-10.13

SAR CoV-2 & Human Proteins interaction

To download all protein-protein docking models please see the Help page

PPI docking	CHARMM_ENERGY	pdb_human	human_genes
2ok3A-nsp12.003.21.min Download Pdb file	-34642.37	2ok3_A	PPIL3
2ok3A-nsp12.001.20.min Download Pdb file	-34603.56	2ok3_A	PPIL3
2ok3A-nsp12.000.02.min Download Pdb file	-34579.55	2ok3_A	PPIL3
2ok3A-nsp12.000.06.min Download Pdb file	-34566.52	2ok3_A	PPIL3

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.