SMTL ID : 8rvb.1

SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 6 residues within 4Å: Chain A: N.17, T.60, L.61, T.62, W.193, C.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.17, A:T.62

1 x 01: (2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[2-(1~{H}-1,2,3-triazol-4-yl)ethylsulfanylmethyl]oxolane-3,4-diol

01.2: 17 residues within 4Å: Chain A: N.47, Y.51, G.75, A.76, G.77, P.84, G.85, D.103, L.104, N.105, G.117, D.118, C.119, D.134, M.135, Y.136, F.153 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.47, A:Y.51, A:G.85, A:L.104, A:N.105, A:D.118, A:C.119, A:D.134, A:Y.136 Water bridges: A:G.75, A:S.78, A:S.78, A:D.103

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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

Kalnins, G. et al., Structural basis for inhibition of the SARS-CoV-2 nsp16 by substrate-based dual site inhibitors. Chemmedchem (2024)

Release Date

2024-02-14

Peptides

2'-O-methyltransferase nsp16: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase nsp16

Non-structural protein 10

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