SMTL ID : 7t48.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 9c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 1 residues within 4Å: Chain A: R.226 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain B: R.226 Ligand excluded by PLIP

2 x FHS: (1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[7-(phenylacetyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid(Covalent)

FHS.2: 19 residues within 4Å: Chain A: H.45, M.53, Y.58, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, Q.193 Ligands: FEY.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.45, A:M.53, A:D.191 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:Q.193 FHS.5: 19 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, Q.193 Ligands: FEY.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:M.53, B:D.191 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

2 x FEY: (1R,2S)-2-{[N-({[(2r,4R)-7-acetyl-7-azaspiro[3.5]non-5-en-2-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

FEY.3: 17 residues within 4Å: Chain A: H.45, M.53, Y.58, F.144, L.145, N.146, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, Q.193 Ligands: FHS.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.45, A:M.53, A:D.191 Hydrogen bonds: A:H.168, A:E.170, A:E.170, A:Q.193 FEY.6: 17 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, L.145, N.146, C.149, H.167, H.168, M.169, E.170, L.171, P.172, H.176, D.191, Q.193 Ligands: FHS.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.45, B:M.53, B:D.191 Hydrogen bonds: B:H.168, B:E.170, B:E.170, B:E.170, B:Q.193

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
A

3C-like proteinase

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