SMTL ID : 8f4y.1

Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: R.89, Q.90, W.91, L.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.92 NA.15: 3 residues within 4Å: Chain B: T.114, L.115, N.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.117

1 x XDU: 4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol(Non-covalent)

XDU.2: 17 residues within 4Å: Chain A: I.71, F.73, S.101, C.118, V.121, H.122, T.123, W.127, M.134, F.152, Y.155, I.156, F.159, K.163, I.293 Ligands: XE0.3, FMT.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.73, A:Y.155, A:I.156 Hydrogen bonds: A:T.123, A:K.163 Water bridges: A:V.121, A:V.121, A:K.163 pi-Stacking: A:F.73, A:F.159

3 x XE0: 4-[2-(2,4-dichlorophenyl)ethyl]-6-(trifluoromethyl)pyrimidin-2-ol(Non-covalent)(Covalent)

XE0.3: 17 residues within 4Å: Chain A: I.71, F.73, S.101, C.118, V.121, H.122, T.123, W.127, M.134, F.152, Y.155, I.156, F.159, K.163, I.293 Ligands: XDU.2, FMT.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.73, A:V.121, A:Y.155, A:I.156, A:F.159, A:F.159 Hydrogen bonds: A:T.123, A:T.123, A:K.163 pi-Stacking: A:F.73 XE0.16: 8 residues within 4Å: Chain B: T.105, C.106, N.108, D.109, G.112, F.113, K.116, Y.129 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.113, B:K.116 Hydrogen bonds: B:T.105 Halogen bonds: B:N.108 XE0.17: 4 residues within 4Å: Chain B: I.41, R.81, C.82, I.84 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.41 Halogen bonds: B:C.82

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

FMT.4: 6 residues within 4Å: Chain A: R.69, N.125, K.126, E.287, N.288, N.289 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:N.125, A:K.126, A:E.287, A:N.289 Water bridges: A:E.287, A:N.289 FMT.5: 7 residues within 4Å: Chain A: Y.135, K.140, T.175, E.176, H.177, S.205 Ligands: FMT.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.175, A:E.176, A:H.177, A:S.205, A:S.205 FMT.6: 3 residues within 4Å: Chain A: S.204, S.205 Ligands: FMT.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.205 Water bridges: A:K.140, A:S.204, A:S.204, A:S.205 FMT.7: 6 residues within 4Å: Chain A: T.139, K.149, E.150, G.151, F.152, F.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.151, A:F.152, A:F.153 Water bridges: A:T.139, A:E.150, A:E.150, A:S.178 FMT.8: 2 residues within 4Å: Chain A: R.258, G.259 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.259 FMT.9: 2 residues within 4Å: Chain A: K.144, E.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.145, A:E.145 FMT.10: 7 residues within 4Å: Chain A: L.103, D.117, C.118, F.152, Y.155 Ligands: XDU.2, XE0.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.118 Water bridges: A:G.116, A:A.119 FMT.11: 4 residues within 4Å: Chain A: S.77, D.78, K.79, V.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:D.78, A:K.79 FMT.12: 2 residues within 4Å: Chain A: N.16, W.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16 FMT.18: 5 residues within 4Å: Chain B: H.51, T.52, G.53, N.65, M.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.66

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain B: C.77, C.80, H.86, C.93 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.77, B:C.80, B:H.86, B:C.93 ZN.14: 4 residues within 4Å: Chain B: C.120, C.123, C.131, C.133 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.120, B:C.123, B:C.131, B:C.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inniss, N.L. et al., Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. Acs Infect Dis. (2023)

Release Date

2023-10-18

Peptides

2'-O-methyltransferase: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase

Non-structural protein 10

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