SMTL ID : 8f4s.1

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 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

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, L.114, 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: FMT.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.73, A:Y.155, A:I.156 Hydrogen bonds: A:T.123 pi-Stacking: A:F.73, A:F.159

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

FMT.3: 4 residues within 4Å: Chain A: C.118, V.121, H.122 Ligands: XDU.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.118, A:H.122 FMT.4: 6 residues within 4Å: Chain A: R.69, N.125, K.126, E.287, N.288, N.289 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:N.125, A:K.126, A:N.289, A:N.289 Water bridges: A:E.287, A:N.289, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.205 Water bridges: A:S.205 FMT.7: 3 residues within 4Å: Chain A: N.32, P.239, Q.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.32 Water bridges: A:I.240, A:L.242

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.9: 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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