SMTL ID : 6w2a.1

1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x VDJ: [4,4-bis(fluoranyl)cyclohexyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate(Covalent)

VDJ.1: 17 residues within 4Å: Chain A: H.48, M.56, F.147, N.149, S.151, C.152, H.170, H.171, M.172, E.173, P.175, H.179, D.194, R.195, Q.196, A.198 Ligands: QYS.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.171, A:E.173, A:E.173, A:E.173, A:Q.196 Water bridges: A:G.150, A:G.150 VDJ.4: 18 residues within 4Å: Chain B: H.48, M.56, F.147, N.149, S.151, C.152, H.170, H.171, M.172, E.173, P.175, H.179, D.194, R.195, Q.196, T.197, A.198 Ligands: QYS.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.48, B:D.194 Hydrogen bonds: B:F.147, B:H.171, B:E.173, B:Q.196, B:Q.196 Water bridges: B:G.150

2 x QYS: (1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

QYS.2: 18 residues within 4Å: Chain A: H.48, M.56, F.147, N.149, G.150, S.151, C.152, H.170, H.171, M.172, E.173, P.175, H.179, D.194, R.195, Q.196, A.198 Ligands: VDJ.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.150, A:S.151, A:S.151, A:C.152, A:H.171, A:E.173, A:E.173, A:E.173, A:Q.196 QYS.3: 19 residues within 4Å: Chain B: H.48, M.56, F.147, N.149, G.150, S.151, C.152, H.170, H.171, M.172, E.173, P.175, H.179, D.194, R.195, Q.196, T.197, A.198 Ligands: VDJ.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.48, B:D.194 Hydrogen bonds: B:F.147, B:G.150, B:S.151, B:C.152, B:H.171, B:E.173, B:Q.196, B:Q.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rathnayake, A.D. et al., 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Sci Transl Med (2020)

Release Date

2020-08-12

Peptides

Replicase polyprotein 1a: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Replicase polyprotein 1a

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