SMTL ID : 7e35.1

Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant bound to compound S43

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.189, C.192, C.224, C.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224, A:C.226 ZN.3: 4 residues within 4Å: Chain B: C.189, C.192, C.224, C.226 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.189, B:C.192, B:C.224, B:C.226

2 x GYX: N-[(3-acetamidophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide(Non-covalent)

GYX.2: 13 residues within 4Å: Chain A: E.161, L.162, G.163, D.164, P.247, P.248, Y.264, N.267, Y.268, Y.273, T.301 Chain B: M.208, Y.268 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.161, A:L.162, A:P.247, A:P.247, A:P.248, A:Y.264, A:Y.268, A:Y.268, A:Y.268, B:M.208, B:Y.268, B:Y.268 Hydrogen bonds: A:Y.268 Salt bridges: A:D.164 GYX.4: 17 residues within 4Å: Chain A: R.166, M.208, G.209, S.245, A.246, P.247, Y.268 Chain B: L.162, D.164, P.247, P.248, Y.264, N.267, Y.268, Q.269, Y.273, T.301 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.162, B:D.164, B:P.247, B:P.248, B:Y.264, B:Y.264, B:Y.268, B:Y.268, B:Y.268, B:T.301, A:Y.268, A:Y.268 Salt bridges: B:D.164 Hydrogen bonds: A:R.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shan, H. et al., Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2. Cell Chem Biol (2021)

Release Date

2021-03-17

Peptides

Non-structural protein 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Non-structural protein 3

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