SMTL ID : 6xmk.1

1.70 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 7j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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.1: 17 residues within 4Å: Chain A: H.45, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, Q.193, T.194, A.195 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:A.195 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:S.148, A:C.149, A:H.168, A:E.170, A:Q.193, A:Q.193 QYS.2: 18 residues within 4Å: Chain B: H.45, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, R.192, Q.193, T.194, A.195 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169 Hydrogen bonds: B:G.147, B:S.148, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 8 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, V.77, L.79, N.99 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.75, B:Q.78, B:T.97

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

2020-07-08

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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