Papain-like proteinase nsp3

UniProt ITasser SWISS Models alphafold D3Targets-2019-nCoV

Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling

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
nsp3

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A 2GRI_A;  6VXS_A;  2W2G_A;  6W9C_A;  2K87_A;  3GA8_A;  1YX1_A;  6ORH_B;  1QWG_A;  3C8F_A;  1HA8_A;  1HUP;  3.22 16.19% 100.00% 1945 Homo 3-mer 

nsp3

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nsp3

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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
pocket92_nsp3 1.99 0.43 64.55 4
pocket93_nsp3 1.87 0.01 2.9 5
pocket140_nsp3 -2.12 0.02 28 6
pocket141_nsp3 -2.2 0.02 33.5 5
pocket109_nsp3 0.65 0 -8.56 7
pocket108_nsp3 0.75 0.01 -7.89 5
pocket49_nsp3 4.09 0.01 -4.33 9
pocket48_nsp3 4.26 0.44 47.57 5
pocket3_nsp3 13.14 0.13 21.96 17
pocket2_nsp3 15.29 0.39 33.23 15
pocket137_nsp3 -2.03 0.02 27.36 3
pocket136_nsp3 -1.84 0.04 39.92 5
pocket77_nsp3 2.62 0.01 -5.1 8
pocket76_nsp3 2.64 0.13 38.69 4
pocket43_nsp3 4.42 0.04 22.64 7
pocket42_nsp3 4.52 0.01 15.71 8
pocket103_nsp3 0.93 0.01 26.9 6
pocket102_nsp3 0.98 0.01 15.4 4
pocket98_nsp3 1.33 0.01 -0.5 7
pocket99_nsp3 1.25 0.01 23.25 7
pocket34_nsp3 4.81 0.02 21.8 6
pocket9_nsp3 8.01 0.05 25.58 7
pocket8_nsp3 8.12 0.02 23.11 12
pocket17_nsp3 6.49 0.26 39.43 11
pocket16_nsp3 6.55 0.03 5.73 7
pocket85_nsp3 2.24 0.01 18.17 8
pocket84_nsp3 2.33 0.04 32.5 6
pocket60_nsp3 3.46 0.01 -0.38 8
pocket61_nsp3 3.38 0.01 -8.4 6
pocket120_nsp3 -0.54 0.13 55 6
pocket121_nsp3 -0.55 0.03 36.71 4
pocket29_nsp3 5.08 0.02 21.8 6
pocket28_nsp3 5.34 0.12 49 7
pocket114_nsp3 0.21 0.01 23.14 7
pocket115_nsp3 -0.02 0.01 -9.33 5
pocket54_nsp3 3.9 0.01 12.64 7
pocket55_nsp3 3.87 0.01 -1.23 9
pocket23_nsp3 5.76 0.1 38.95 7
pocket22_nsp3 5.85 0.01 15.71 8
pocket119_nsp3 -0.29 0.01 24.13 5
pocket118_nsp3 -0.29 0.01 24.13 5
pocket59_nsp3 3.51 0.07 35.57 4
pocket58_nsp3 3.62 0.2 51.33 5
pocket82_nsp3 2.37 0.25 57.4 3
pocket83_nsp3 2.33 0.02 32.55 7
pocket10_nsp3 8.01 0.02 23.11 12
pocket11_nsp3 7.67 0.04 25.58 7
pocket127_nsp3 -0.78 0.41 65 4
pocket126_nsp3 -0.75 0.06 28.04 9
pocket67_nsp3 3.01 0.04 37 5
pocket66_nsp3 3.08 0.06 28.88 9
pocket88_nsp3 2.08 0.03 39 5
pocket89_nsp3 2.07 0.03 39 5
pocket53_nsp3 3.91 0.01 12.64 7
pocket52_nsp3 3.93 0.06 44.62 7
pocket113_nsp3 0.35 0.01 23.14 7
pocket112_nsp3 0.36 0.01 3.43 6
pocket24_nsp3 5.67 0.09 38.95 7
pocket25_nsp3 5.6 0.01 18.35 11
pocket95_nsp3 1.7 0.37 59.23 10
pocket94_nsp3 1.73 0.01 23.9 6
pocket147_nsp3 -3.88 0.01 16.11 3
pocket146_nsp3 -3.4 0.04 45.8 2
pocket39_nsp3 4.65 0.31 43.39 8
pocket4_nsp3 12.5 0.07 21.06 14
pocket38_nsp3 4.75 0.01 2.41 12
pocket5_nsp3 12.41 0.16 33.23 15
pocket70_nsp3 2.95 0.14 38.69 4
pocket71_nsp3 2.95 0.04 37 5
pocket130_nsp3 -1.08 0.01 14.3 6
pocket131_nsp3 -1.3 0.01 29.25 4
pocket104_nsp3 0.86 0.01 14.1 6
pocket105_nsp3 0.86 0.01 14.1 6
pocket44_nsp3 4.41 0.01 9.42 7
pocket45_nsp3 4.33 0.45 47.57 5
pocket33_nsp3 4.89 0.08 37 7
pocket32_nsp3 4.99 0.02 11.28 12
pocket117_nsp3 -0.23 0.02 26.67 5
pocket116_nsp3 -0.07 0.01 11.5 3
pocket57_nsp3 3.86 0.02 28 10
pocket56_nsp3 3.86 0.02 28 10
pocket20_nsp3 6.13 0.03 34.36 8
pocket21_nsp3 6.03 0.01 1.87 10
pocket129_nsp3 -0.93 0.04 37.53 6
pocket128_nsp3 -0.89 0.02 26.11 5
pocket69_nsp3 2.97 0.08 35.57 4
pocket68_nsp3 3 0.04 37 5
pocket14_nsp3 7.08 0.07 35.92 8
pocket15_nsp3 6.77 0.04 5.73 7
pocket86_nsp3 2.2 0.08 39.38 4
pocket87_nsp3 2.2 0.08 39.38 4
pocket63_nsp3 3.38 0.07 30.69 9
pocket62_nsp3 3.38 0.33 47.57 5
pocket123_nsp3 -0.61 0.01 18.11 7
pocket122_nsp3 -0.6 0.46 66.68 4
pocket40_nsp3 4.62 0.21 40.47 8
pocket41_nsp3 4.58 0.06 44.62 7
pocket100_nsp3 1.05 0.09 43.2 4
pocket101_nsp3 0.99 0.09 50.62 5
pocket148_nsp3 -3.94 0.02 30 6
pocket37_nsp3 4.8 0.03 23.45 7
pocket36_nsp3 4.8 0.03 23.45 7
pocket91_nsp3 1.99 0.43 64.55 4
pocket90_nsp3 2 0.43 64.55 4
pocket143_nsp3 -2.51 0.02 33.5 5
pocket142_nsp3 -2.28 0.01 20.64 6
pocket0_nsp3 36.62 0.66 17.5 26
pocket1_nsp3 16.77 0.06 2.89 19
pocket134_nsp3 -1.38 0 -12.78 6
pocket135_nsp3 -1.74 0.01 17.89 3
pocket74_nsp3 2.83 0.3 57.4 3
pocket75_nsp3 2.7 0.02 27.9 6
pocket107_nsp3 0.76 0.03 35 4
pocket106_nsp3 0.85 0.01 14.1 6
pocket47_nsp3 4.28 0.01 10.62 8
pocket46_nsp3 4.3 0.07 40.1 7
pocket139_nsp3 -2.12 0.02 28 6
pocket138_nsp3 -2.12 0.02 28 6
pocket79_nsp3 2.53 0.02 5.09 7
pocket78_nsp3 2.58 0.01 20.15 7
pocket30_nsp3 5.05 0.02 25.06 9
pocket31_nsp3 5.05 0.02 25.06 9
pocket96_nsp3 1.59 0.12 50.62 5
pocket97_nsp3 1.34 0.02 25.33 5
pocket144_nsp3 -3.33 0.01 16.11 3
pocket145_nsp3 -3.4 0.01 16.11 3
pocket7_nsp3 8.57 0.01 14.73 12
pocket6_nsp3 9.12 0.04 28.21 17
pocket73_nsp3 2.91 0.51 61.11 3
pocket72_nsp3 2.93 0.33 39.25 2
pocket133_nsp3 -1.36 0.04 25.6 3
pocket132_nsp3 -1.31 0.01 29.25 4
pocket19_nsp3 6.15 0.04 5.73 7
pocket18_nsp3 6.35 0.13 54.81 10
pocket50_nsp3 4.06 0.33 53.18 5
pocket51_nsp3 4.01 0.69 61.11 3
pocket110_nsp3 0.63 0.03 35 4
pocket111_nsp3 0.48 0.03 35 4
pocket27_nsp3 5.47 0.12 49 7
pocket26_nsp3 5.53 0.04 37.7 7
pocket81_nsp3 2.38 0.09 45.36 6
pocket80_nsp3 2.51 0.01 0.56 7
pocket13_nsp3 7.55 0.06 35.92 8
pocket12_nsp3 7.63 0.04 25.58 7
pocket124_nsp3 -0.62 0.01 18.11 7
pocket125_nsp3 -0.66 0.01 18.11 7
pocket64_nsp3 3.37 0.01 14.18 9
pocket65_nsp3 3.18 0.06 35.57 4

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Other PDB Hits

ID Method Resolution Å Chains Links
7jrn X-RAY 2.48 A PDBe
RCSB PDB
7d6h X-RAY 1.6 A PDBe
RCSB PDB
7d7t X-RAY 3.15 A PDBe
RCSB PDB
7jvz X-RAY 2.5 A; PDBe
RCSB PDB
7cx9 X-RAY 1.73 A; PDBe
RCSB PDB
7cjd X-RAY 2.5 D, A, B, C; PDBe
RCSB PDB
7cmd X-RAY 2.59 A, B, C, D; PDBe
RCSB PDB
7jme X-RAY 1.55 A; PDBe
RCSB PDB
7cjm X-RAY 3.2 B; PDBe
RCSB PDB
7jn2 X-RAY 1.93 A PDBe
RCSB PDB
6ywm X-RAY 2.16 A PDBe
RCSB PDB
6ywl X-RAY 2.5 A PDBe
RCSB PDB
6ywk X-RAY 2.2 A PDBe
RCSB PDB
6woj X-RAY 2.2 A PDBe
RCSB PDB
6wey X-RAY 0.95 A PDBe
RCSB PDB
6wcf X-RAY 1.06 A PDBe
RCSB PDB
6wen X-RAY 1.35 A PDBe
RCSB PDB
6vxs X-RAY 2.03 A PDBe
RCSB PDB
6w6y X-RAY 1.45 A PDBe
RCSB PDB
6w02 X-RAY 1.5 A PDBe
RCSB PDB
6wrh X-RAY 1.6 A PDBe
RCSB PDB
6wzu X-RAY 1.79 A PDBe
RCSB PDB
6w9c X-RAY 2.7 A,B,C PDBe
RCSB PDB
6wx4 X-RAY 1.66 D,I PDBe
RCSB PDB
6yva X-RAY 3.18 A,C PDBe
RCSB PDB
6wuu X-RAY 2.79 A,B,C,D,G,H,I,J PDBe
RCSB PDB
6xg3 X-RAY 2.48 A PDBe
RCSB PDB
6xaa X-RAY 2.7 A,B PDBe
RCSB PDB
7jir X-RAY 2.09 A; PDBe
RCSB PDB
7jit X-RAY 1.95 A; PDBe
RCSB PDB
7jiw X-RAY 2.3 A; PDBe
RCSB PDB
7jiv X-RAY 2.05 A; PDBe
RCSB PDB
6xa9 X-RAY 2.9 A,B,C,D,E,F PDBe
RCSB PDB
7d47 X-RAY 1.97 A, B; PDBe
RCSB PDB
7kag X-RAY 3.21 A, B; PDBe
RCSB PDB
7kg3 X-RAY 1.45 A; PDBe
RCSB PDB

Predictions of Mutations

pdb_id mutations deepddg maestro mCSM_ppi mCSM_Stability imutant provean
6vww A114F 1.02 -0.217 -1.174 -1.072 Decrease -2.576
6w9c A114I 0.623 -0.055 -1.465 -0.341 Increase -0.707
6w9c A114L 1.133 -0.412 -1.465 -0.341 Decrease -1.361
6w9c A114M 0.585 0.072 -1.276 -0.473 Decrease -1.395
6w9c A114W -0.165 -0.04 -1.378 -1.614 Decrease -3.508
6w9c A114Y -1.872 0.15 -1.208 -1.15 Decrease -2.595
6w9c A139F 1.863 0.116 -1.03 -0.809 Decrease -1.626
6w9c A139I -0.508 0.209 -1.298 0.048 Decrease -0.702
6w9c A139L 1.165 0.109 -1.298 0.048 Decrease -1.358
6w9c A139M 0.077 0.214 -0.963 -0.249 Decrease -1.039
6w9c A139W 0.9 -0.1 -1.205 -1.435 Decrease -2.685
6w9c A139Y 1.298 0.024 -1.041 -0.906 Decrease -1.126
6w9c K92A -0.585 0.103 -0.394 -0.124 Decrease -0.242
6w9c K92C -1.123 0.144 -0.023 -0.119 Increase -1.376
6w9c K92D -1.115 0.008 -0.008 0.219 Increase 0.066
6w9c K92E -0.665 -0.191 -0.066 0.259 Decrease 0.102
6w9c K92F -0.711 0.211 -0.226 -0.145 Increase -0.877
6w9c K92G -1.269 -0.087 -0.376 -0.384 Decrease -1.227
6w9c K92I -0.323 0.055 -0.456 0.498 Decrease -0.78
6w9c K92L -0.655 0.004 -0.456 0.498 Increase -0.694
6w9c K92M -0.483 -0.11 0.197 0.301 Increase -0.581
6w9c K92N -1.216 -0.162 -0.56 0.224 Decrease -0.221
6w9c K92P -1.046 -0.194 -0.434 0.32 Increase 0.234
6w9c K92Q -0.227 -0.396 -0.389 0.092 Increase -0.251
6w9c K92R -0.209 -0.12 -0.587 -0.105 Decrease -0.566
6w9c K92S -0.634 -0.286 -0.396 -0.333 Decrease -0.011
6w9c K92T -0.925 0.149 -0.417 -0.123 Increase 0.143
6w9c K92V -0.961 0.091 -0.434 0.32 Increase -0.577
6w9c K92W -0.786 0.099 -0.104 -0.116 Decrease -1.811
6w9c K92Y -0.847 0.236 -0.13 0.205 Increase -1.158
6w9c M23W -0.746 -0.175 -0.51 -0.783 Increase -1.489
6w9c M23Y -1.152 0.035 -0.598 -0.747 Increase -0.271
6w9c N13E -0.868 -0.082 -0.362 0.119 Increase -0.268
6w9c N13F -0.588 0.188 -1.197 -0.859 Increase -2.36
6w9c N13K -0.828 0.265 -0.438 -0.098 Decrease -0.793
6w9c N13L -0.688 0.196 -0.677 -0.222 Increase -1.758
6w9c N13M -0.544 0.157 0.111 0.122 Increase -1.735
6w9c N13Q -0.47 -0.001 -0.4 -0.619 Decrease -0.925
6w9c N13W -0.243 -0.206 -1.404 -0.597 Increase -2.65
6w9c N13Y -0.492 0.025 -1.125 -0.41 Decrease -1.917
6w9c R138A -0.718 0.151 -0.245 -0.541 Decrease -1.857
6w9c R138E -0.09 -0.038 0.236 -0.073 Decrease -0.861
6w9c R138G -1.59 0.101 -0.169 -0.814 Decrease -2.575
6w9c R138K -0.487 -0.21 0.1 -0.606 Decrease 1.246
6w9c R138M -0.459 0.115 -0.011 -0.027 Increase -1.288
6w9c R138N -0.874 -0.122 0.203 -0.053 Decrease -1.277
6w9c R138P -1.774 -0.082 -0.405 -0.045 Decrease -2.448
6w9c R138Q -0.533 -0.091 0.191 -0.288 Decrease -0.481
6w9c R138S -0.703 -0.311 0.367 -0.703 Decrease -1.283
6w9c R138W -0.718 0.21 -0.047 -0.373 Decrease -2.752

Virtual Screening ligands Docking

Docking Structure pdb Ligand Name glide_gscore MMGBSA_ΔG_Bind docking_score
NSP-3-6XAA-FDA_1

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 6XAA MEROPENEM -7.01 -17.41 -6.98
NSP-3-6XAA-FDA_2

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 6XAA MITOXANTRONE -5.81 -28.25 -5.81
NSP-3-6XAA-FDA_3

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 6XAA MIGALASTAT -5.67 -26.34 -5.66
NSP-3-6XAA-FDA_4

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 6XAA METAPROTERENOL -5.42 -20.42 -5.41
NSP-3-6XAA-FDA_5

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 6XAA METARAMINOL -5.4 -23.71 -5.38

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.





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