SMTL ID : 7jkv.1

Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x V7G: N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide(Covalent)

V7G.1: 20 residues within 4Å: Chain A: T.26, H.42, M.50, F.141, L.142, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, P.169, H.173, D.188, R.189, Q.190, T.191, A.192 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.26, A:P.169, A:A.192 Hydrogen bonds: A:F.141, A:G.144, A:S.145, A:S.145, A:C.146, A:H.165, A:E.167, A:E.167, A:Q.190 Water bridges: A:Q.190 V7G.2: 18 residues within 4Å: Chain B: T.26, L.28, H.42, M.50, F.141, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, P.169, H.173, Q.190, T.191, A.192 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.26, B:P.169, B:A.192 Hydrogen bonds: B:F.141, B:G.144, B:S.145, B:S.145, B:C.146, B:H.165, B:E.167, B:E.167, B:Q.190 Water bridges: B:Q.190

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 9 residues within 4Å: Chain B: E.15, G.16, M.18, W.32, A.71, V.74, L.76, N.96, K.98 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.72, B:K.98, B:K.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, S.I. et al., A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun (2021)

Release Date

2020-09-23

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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