Uridylate-specific endoribonuclease nsp15

UniProt ITasser SWISS Models alphafold D3Targets-2019-nCoV

Mn2+-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond

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_6VWW

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A,B 6VWW; Solved experimentally with good Coverage;  NA 100% 0.00% 346 Homo 6-mer

NA

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NA

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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
pocket0_nsp15 37.9 0.07 11.26 14
pocket1_nsp15 33.65 0.64 38.93 9
pocket2_nsp15 31.5 0.04 10.5 12
pocket3_nsp15 30.55 0.03 18.5 11
pocket4_nsp15 30.38 0.03 9.47 11
pocket5_nsp15 29.41 0.04 27.65 8
pocket6_nsp15 26.17 0.04 27.65 8
pocket7_nsp15 24.42 0.08 42.54 7
pocket8_nsp15 24.42 0.06 32.77 8
pocket9_nsp15 24.33 0.04 35.18 7
pocket10_nsp15 21.88 0.02 21.08 6
pocket11_nsp15 21.77 0.03 23.23 10
pocket12_nsp15 21.63 0.03 23.23 10
pocket13_nsp15 21.54 0.54 66.38 4
pocket14_nsp15 20.79 0.06 39.45 7
pocket15_nsp15 18.57 0.01 5.08 7
pocket16_nsp15 16.96 0.02 17.44 7
pocket17_nsp15 16.95 0.33 28 1
pocket18_nsp15 16.86 0.02 26.91 5
pocket19_nsp15 16.55 0.06 37.91 4
pocket20_nsp15 16.46 0.02 26.91 5
pocket21_nsp15 16.24 0.02 14.83 5
pocket22_nsp15 16.06 0.01 10.42 7
pocket23_nsp15 15.43 0.01 21.08 6
pocket24_nsp15 15.35 0.03 30.5 7
pocket25_nsp15 14.2 0.43 50.62 3
pocket26_nsp15 13.57 0.03 38.25 4
pocket27_nsp15 12.87 0.07 46.63 4
pocket28_nsp15 12.55 0.02 29.21 6
pocket29_nsp15 12.13 0.21 65 4
pocket30_nsp15 11.67 0.01 18.5 7
pocket31_nsp15 11.59 0.06 43.63 3
pocket32_nsp15 11.36 0.13 49.25 2
pocket33_nsp15 10.88 0.16 40.42 2
pocket34_nsp15 10.26 0.06 46.89 4
pocket35_nsp15 9.88 0.01 20.78 5

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Other PDB Hits

ID Method Resolution Å Chains Links
6xdh X-RAY 2.35 A,B PDBe
RCSB PDB
6x1b X-RAY 1.97 A,B PDBe
RCSB PDB
6wxc X-RAY 1.85 A,B PDBe
RCSB PDB
6w01 X-RAY 1.9 A,B PDBe
RCSB PDB
6x1b X-RAY 1.97 A,B,D,F PDBe
RCSB PDB
6wlc X-RAY 1.82 A,B PDBe
RCSB PDB
6vww X-RAY 2.2 A,B PDBe
RCSB PDB
6X4I X-RAY 1.85 A,B PDBe
RCSB PDB
7k9p X-RAY 2.6 A, B; PDBe
RCSB PDB
7k1l X-RAY 2.25 A, B; PDBe
RCSB PDB
7k1o X-RAY 2.4 A, B, C; PDBe
RCSB PDB

Predictions of Mutations

pdb_id mutations deepddg maestro mCSM_ppi mCSM_Stability imutant provean
6vww A82F 0.698 -1.205 -0.636 -0.646 Decrease 1.222
6vww A82I -0.593 -1.202 -1.108 0.248 Decrease -0.487
6vww A82L -0.027 -1.088 -1.108 0.248 Decrease -0.431
6vww A82M -0.764 -1.168 -1.001 0.121 Decrease 0.055
6vww A82V -0.273 -0.896 -1 -0.076 Decrease -0.36
6vww A82W 1.041 -0.965 -0.695 -1.366 Decrease 2.755
6vww A82Y 1.435 -0.985 -0.625 -0.774 Decrease 2.904
6vww F124I -3.159 -0.896 -0.394 -1.408 Decrease -3.059
6vww F124L -3.478 -1.043 -0.394 -1.408 Decrease -3.092
6vww F124V -3.634 -0.578 -0.301 -1.868 Decrease -3.294
6vww G248C -2.31 -0.558 -0.951 -1.35 Decrease -4.231
6vww G248F -3.002 -1.057 -0.166 -1.035 Decrease -4.386
6vww G248I -2.405 -0.83 -0.557 -0.241 Increase -5.784
6vww G248L -3.216 -0.761 -0.557 -0.241 Decrease -5.784
6vww G248M -2.495 -0.825 -0.692 -0.262 Increase -5.138
6vww G248W -2.045 -0.726 -0.445 -1.639 Decrease -4.762
6vww G248Y -1.985 -0.772 -0.109 -1.187 Increase -4.598
6vww K182C -2.368 -0.941 -1.106 -1.867 Increase -2.375
6vww K182F -0.447 -1.247 -1.07 -0.957 Increase -1.797
6vww K182H -1.896 -0.956 0.233 -2.173 Decrease -1.11
6vww K182I -0.217 -1.279 -0.955 -0.467 Increase -2.728
6vww K182L -0.801 -1.322 -0.955 -0.467 Increase -2.483
6vww K182M -1.049 -1.3 -1.029 -0.873 Increase -1.955
6vww K182P -4.342 -0.595 -0.882 -0.796 Increase -1.355
6vww K182Q -3.399 -0.766 -0.61 -1.567 Increase -0.867
6vww K182R 1.341 -0.881 -0.954 -1.427 Increase 0.643
6vww K182T -2.018 -0.658 -0.781 -1.809 Increase -1.771
6vww K182V -1.072 -0.935 -1.028 -0.757 Increase -2.53
6vww K182W 0.075 -1.588 -1.141 -1.113 Increase -2.311
6vww K182Y -0.928 -1.377 -0.847 -0.789 Increase -0.572
6vww L299W -0.692 -0.76 0.032 -1.593 Decrease -3.255
6vww S289A -1.253 -0.618 -0.117 -0.859 Decrease -0.902
6vww S289C -0.251 -1.257 -0.333 -0.799 Decrease -2.239
6vww S289F -0.113 -1.435 -0.426 -1.241 Decrease -2.806
6vww S289H -1.607 -1.061 0.238 -1.516 Decrease -2.584
6vww S289I -0.737 -0.945 -0.438 -0.432 Increase -2.997
6vww S289L -0.911 -0.922 -0.438 -0.432 Decrease -2.964
6vww S289M -0.558 -1.303 -0.175 -0.079 Decrease -2.415
6vww S289T -1.54 -0.595 -0.558 -0.754 Decrease -1.238
6vww S289V -0.795 -0.956 -0.321 -0.545 Decrease -2.88
6vww S289W 0.158 -1.327 -0.388 -1.2 Decrease -3.552
6vww S289Y 0.432 -1.279 -0.233 -0.893 Decrease -2.634
6vww V11E -3.494 -0.649 -0.263 -0.436 Decrease -3.04
6vww V319F -0.793 -1.024 -0.749 -0.849 Decrease -0.255
6vww V319I -0.302 -0.638 -0.999 -0.266 Decrease -0.306
6vww V319L -1.363 -0.81 -0.944 -0.152 Decrease -0.857
6vww V319W -1.514 -0.989 -0.972 -1.332 Decrease -1.489
6vww V319Y -1.297 -0.869 -0.855 -0.915 Decrease 0.733
6vww Y180F -1.157 -0.813 -0.589 -0.919 Increase -0.607
6vww Y180I -3.685 -0.946 -0.683 -1.125 Decrease -0.126
6vww Y180L -3.057 -1.109 -0.801 -1.398 Increase -0.705
6vww Y180W -3.006 -0.593 -1.338 -0.138 Decrease -1.255

Virtual Screening ligands Docking

Docking Structure pdb Ligand Name glide_gscore MMGBSA_ΔG_Bind docking_score
NSP-15-6XDH-FDA_1

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 6XDH MIRABEGRON -9.1 -45.9 -8.25
NSP-15-6XDH-FDA_2

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 6XDH PROTOKYLOL -7.72 -49.47 -7.71
NSP-15-6XDH-FDA_3

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 6XDH MITOXANTRONE -6.56 -55.57 -6.56
NSP-15-6XDH-FDA_4

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 6XDH CANAGLIFLOZIN -6.54 -46.62 -6.54
NSP-15-6XDH-FDA_5

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 6XDH DOBUTAMINE -6.5 -41.11 -6.5

SAR CoV-2 & Human Proteins interaction

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

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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