SMTL ID : 7t4b.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 14c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x FWI: (1R,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid(Covalent)

FWI.1: 17 residues within 4Å: Chain A: H.45, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, Q.193, T.194, A.195 Ligands: FZI.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:D.191 Hydrogen bonds: A:F.144, A:S.148, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147, A:G.147 FWI.4: 16 residues within 4Å: Chain B: H.45, M.53, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193, T.194 Ligands: FZI.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169 Hydrogen bonds: B:F.144, B:S.148, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193 Water bridges: B:G.147

2 x FZI: (1S,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid(Covalent)

FZI.2: 18 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 Ligands: FWI.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.191 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 FZI.5: 18 residues within 4Å: Chain B: H.45, M.53, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, R.192, Q.193, T.194 Ligands: FWI.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169 Hydrogen bonds: B:F.144, 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: 9 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, V.77, L.79, N.99, K.101 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.75, B:Q.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J.Med.Chem. (2022)

Release Date

2021-12-22

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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