SMTL ID : 8rv6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

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

MES.1: 5 residues within 4Å: Chain A: N.17, T.60, L.61, T.62, W.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.17, A:T.62

1 x 01: 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(4-hydroxyphenyl)benzoic acid

01.2: 13 residues within 4Å: Chain A: G.75, G.77, D.103, L.104, N.105, G.117, D.118, C.119, D.134, M.135, Y.136, P.138, F.153 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.136, A:Y.136, A:P.138 Hydrogen bonds: A:L.104, A:N.105, A:D.118, A:C.119, A:Y.136 Water bridges: A:G.75, A:S.78, A:D.103, A:F.153

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.70, N.126, K.127, R.287, E.288, N.289, N.290 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.70, A:R.70, A:K.127, A:E.288, A:N.290, A:N.290 GOL.4: 6 residues within 4Å: Chain A: V.122, H.123, T.124, F.160, Q.163, K.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.124, A:T.124 GOL.7: 7 residues within 4Å: Chain B: I.41, T.42, N.43, C.44, F.71, A.107, P.110 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.41, B:N.43, B:C.44, B:A.107

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.6: 5 residues within 4Å: Chain B: C.120, V.122, C.123, C.131, C.133 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.120, B:C.123, B:C.131, B:C.133, H2O.6

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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