SMTL ID : 9hh6.1

Crystal Structure of Nsp15 Endoribonuclease from SARS CoV-2 in Complex with TAS-103

Coordinates

PDB Format Compare

Method

SOLUTION SCATTERING 2.00 Å

Oligo State

hetero-3-3-mer

Ligands

6 x 01: 6-[2-(dimethylamino)ethylamino]-3-oxidanyl-indeno[2,1-c]quinolin-7-one

01.1: 7 residues within 4Å: Chain A: F.205, K.206, P.207, I.213, L.216, E.217, K.261 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.206, A:P.207, A:L.216, A:E.217 Hydrogen bonds: A:K.206 01.7: 7 residues within 4Å: Chain B: F.205, K.206, P.207, I.213, L.216, E.217, K.261 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.206, B:P.207, B:L.216, B:E.217 Hydrogen bonds: B:K.206 01.11: 7 residues within 4Å: Chain C: F.205, K.206, P.207, I.213, L.216, E.217, K.261 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.206, C:P.207, C:L.216, C:E.217 Hydrogen bonds: C:K.206 01.17: 7 residues within 4Å: Chain D: F.205, K.206, P.207, I.213, L.216, E.217, K.261 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.206, D:P.207, D:L.216, D:E.217 Hydrogen bonds: D:K.206 01.21: 7 residues within 4Å: Chain E: F.205, K.206, P.207, I.213, L.216, E.217, K.261 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:K.206, E:P.207, E:L.216, E:E.217 Hydrogen bonds: E:K.206 01.27: 7 residues within 4Å: Chain F: F.205, K.206, P.207, I.213, L.216, E.217, K.261 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:K.206, F:P.207, F:L.216, F:E.217 Hydrogen bonds: F:K.206

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

PO4.2: 6 residues within 4Å: Chain A: H.236, G.248, G.249, H.251, K.291, T.342 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.249, A:T.342 Water bridges: A:K.291, A:K.291 Salt bridges: A:H.236, A:H.251, A:K.291 PO4.8: 6 residues within 4Å: Chain B: H.236, G.248, G.249, H.251, K.291, T.342 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.249, B:T.342 Salt bridges: B:H.236, B:H.251, B:K.291 PO4.12: 6 residues within 4Å: Chain C: H.236, G.248, G.249, H.251, K.291, T.342 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.249, C:T.342 Water bridges: C:K.291, C:K.291 Salt bridges: C:H.236, C:H.251, C:K.291 PO4.18: 6 residues within 4Å: Chain D: H.236, G.248, G.249, H.251, K.291, T.342 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.249, D:T.342 Salt bridges: D:H.236, D:H.251, D:K.291 PO4.22: 6 residues within 4Å: Chain E: H.236, G.248, G.249, H.251, K.291, T.342 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.249, E:T.342 Water bridges: E:K.291, E:K.291 Salt bridges: E:H.236, E:H.251, E:K.291 PO4.28: 6 residues within 4Å: Chain F: H.236, G.248, G.249, H.251, K.291, T.342 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.249, F:T.342 Salt bridges: F:H.236, F:H.251, F:K.291

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

EDO.3: 4 residues within 4Å: Chain A: L.44, F.45, E.46, W.60 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: E.5, P.25, V.26 Chain D: N.54, E.58, C.104, S.105, M.106 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: N.54, E.58, C.104, S.105, M.106 Chain D: E.5, P.25, V.26 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: N.76, L.77, K.182, L.191, P.192, Y.326 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain B: V.150, K.151, G.152 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: L.44, F.45, E.46, W.60 Chain F: E.268 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: L.44, F.45, E.46, W.60 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain C: E.5, P.25, V.26 Chain F: N.54, E.58, C.104, S.105, M.106 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain C: N.54, E.58, C.104, S.105, M.106 Chain F: E.5, P.25, V.26 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain C: N.76, L.77, K.182, L.191, P.192, Y.326 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain D: V.150, K.151, G.152 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: E.268 Chain D: L.44, F.45, E.46, W.60 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain E: L.44, F.45, E.46, W.60 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain B: N.54, E.58, C.104, S.105, M.106 Chain E: E.5, P.25, V.26 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain B: E.5, P.25, V.26 Chain E: N.54, E.58, C.104, S.105, M.106 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain E: N.76, L.77, K.182, L.191, P.192, Y.326 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain F: V.150, K.151, G.152 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: E.268 Chain F: L.44, F.45, E.46, W.60 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chatziefthymiou, S.D. et al., Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15. Protein Sci. (2025)

Release Date

2025-05-28

Peptides

ORF1ab polyprotein: ACE
ORF1ab polyprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

ORF1ab polyprotein

ORF1ab polyprotein

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