SMTL ID : 6wxc.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with potential repurposing drug Tipiracil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x CMU: 5-CHLORO-6-(1-(2-IMINOPYRROLIDINYL) METHYL) URACIL(Non-covalent)

CMU.1: 9 residues within 4Å: Chain A: Q.268, H.273, K.313, V.315, C.316, S.317, Y.366, K.368 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.268, A:S.317, A:S.317, A:S.317 pi-Stacking: A:Y.366 CMU.11: 9 residues within 4Å: Chain B: Q.268, H.273, K.313, V.315, C.316, S.317, Y.366, K.368 Ligands: PO4.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.268, B:S.317, B:S.317, B:S.317 pi-Stacking: B:Y.366 CMU.18: 9 residues within 4Å: Chain C: Q.268, H.273, K.313, V.315, C.316, S.317, Y.366, K.368 Ligands: PO4.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.268, C:S.317, C:S.317, C:S.317 pi-Stacking: C:Y.366 CMU.28: 9 residues within 4Å: Chain D: Q.268, H.273, K.313, V.315, C.316, S.317, Y.366, K.368 Ligands: PO4.29 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.268, D:S.317, D:S.317, D:S.317 pi-Stacking: D:Y.366 CMU.35: 9 residues within 4Å: Chain E: Q.268, H.273, K.313, V.315, C.316, S.317, Y.366, K.368 Ligands: PO4.36 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.268, E:S.317, E:S.317, E:S.317 pi-Stacking: E:Y.366 CMU.45: 9 residues within 4Å: Chain F: Q.268, H.273, K.313, V.315, C.316, S.317, Y.366, K.368 Ligands: PO4.46 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.268, F:S.317, F:S.317, F:S.317 pi-Stacking: F:Y.366

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: H.258, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: CMU.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.271, A:T.364 Salt bridges: A:H.258, A:H.273, A:K.313 PO4.12: 7 residues within 4Å: Chain B: H.258, G.270, G.271, H.273, K.313, T.364 Ligands: CMU.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.271 Water bridges: B:H.258, B:Q.268, B:Q.268 Salt bridges: B:H.258, B:H.273, B:K.313 PO4.19: 8 residues within 4Å: Chain C: H.258, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: CMU.18 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.271, C:T.364 Salt bridges: C:H.258, C:H.273, C:K.313 PO4.29: 7 residues within 4Å: Chain D: H.258, G.270, G.271, H.273, K.313, T.364 Ligands: CMU.28 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.271 Water bridges: D:H.258, D:Q.268, D:Q.268 Salt bridges: D:H.258, D:H.273, D:K.313 PO4.36: 8 residues within 4Å: Chain E: H.258, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: CMU.35 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.271, E:T.364 Salt bridges: E:H.258, E:H.273, E:K.313 PO4.46: 7 residues within 4Å: Chain F: H.258, G.270, G.271, H.273, K.313, T.364 Ligands: CMU.45 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.271 Water bridges: F:H.258, F:Q.268, F:Q.268 Salt bridges: F:H.258, F:H.273, F:K.313

27 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: E.27, P.47, V.48 Chain F: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: N.76, E.80, C.126, S.127, M.128 Chain F: E.27, P.47, V.48 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: V.101, D.102, A.118, H.119, I.120 Chain C: V.62 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: G.193, E.194, V.196, K.197 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: N.98, L.99, G.100, K.204, L.213, P.214, Y.348 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: S.171, V.172, K.173, G.174, L.175 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: F.67, E.68, K.70, W.82, W.110, D.115 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: N.76, E.80, C.126, S.127, M.128 Chain C: E.27, P.47, V.48 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: E.27, P.47, V.48 Chain C: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain C: V.101, D.102, A.118, H.119, I.120 Chain E: V.62 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: G.193, E.194, V.196, K.197 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain C: N.98, L.99, G.100, K.204, L.213, P.214, Y.348 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: S.171, V.172, K.173, G.174, L.175 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain D: F.67, E.68, K.70, W.82, W.110, D.115 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain E: L.66, F.67, E.68, W.82 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain D: N.76, E.80, C.126, S.127, M.128 Chain E: E.27, P.47, V.48 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain D: E.27, P.47, V.48 Chain E: N.76, E.80, C.126, S.127, M.128 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain A: V.62 Chain E: V.101, D.102, A.118, H.119, I.120 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain E: G.193, E.194, V.196, K.197 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain E: N.98, L.99, G.100, K.204, L.213, P.214, Y.348 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain E: L.335, S.336, V.337, V.338, C.357, K.358, D.359, G.360 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain F: S.171, V.172, K.173, G.174, L.175 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain F: F.67, E.68, K.70, W.82, W.110, D.115 Ligand excluded by PLIP

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.9: 3 residues within 4Å: Chain A: H.266, S.267 Chain C: A.195 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.267, C:A.195 Water bridges: A:Q.268 FMT.14: 4 residues within 4Å: Chain B: V.179, E.215, T.216, F.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.216, B:T.216 Water bridges: B:V.179 FMT.15: 5 residues within 4Å: Chain B: G.149, T.168, E.169, G.170, S.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.169, B:G.170, B:S.171 FMT.16: 1 residues within 4Å: Chain B: S.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.171 Water bridges: B:S.171, B:S.171 FMT.26: 3 residues within 4Å: Chain C: H.266, S.267 Chain E: A.195 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:A.195, C:S.267 Water bridges: C:Q.268 FMT.31: 4 residues within 4Å: Chain D: V.179, E.215, T.216, F.218 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.216, D:T.216 Water bridges: D:V.179 FMT.32: 5 residues within 4Å: Chain D: G.149, T.168, E.169, G.170, S.171 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.169, D:G.170, D:S.171 FMT.33: 1 residues within 4Å: Chain D: S.171 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.171 Water bridges: D:S.171, D:S.171 FMT.43: 3 residues within 4Å: Chain A: A.195 Chain E: H.266, S.267 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.267, A:A.195 Water bridges: E:Q.268 FMT.48: 4 residues within 4Å: Chain F: V.179, E.215, T.216, F.218 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.216, F:T.216 Water bridges: F:V.179 FMT.49: 5 residues within 4Å: Chain F: G.149, T.168, E.169, G.170, S.171 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.169, F:G.170, F:S.171 FMT.50: 1 residues within 4Å: Chain F: S.171 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.171 Water bridges: F:S.171, F:S.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Commun Biol (2021)

Release Date

2020-05-20

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uridylate-specific endoribonuclease

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