SMTL ID : 7t4a.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 11c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

EQS.1: 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, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: EO6.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:M.169, A:E.170 Hydrogen bonds: A:F.144, A:G.147, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 EQS.4: 14 residues within 4Å: Chain B: H.45, F.144, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193 Ligands: EO6.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169, B:E.170 Hydrogen bonds: B:G.147, B:C.149, B:H.168, B:E.170, B:E.170, B:E.170, B:Q.193, B:Q.193

2 x EO6: (1R,2S)-2-[(N-{[(7-cyano-7-azaspiro[3.5]nonan-2-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

EO6.2: 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, L.171, P.172, H.176, D.191, R.192, Q.193 Ligands: EQS.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:M.169, A:E.170 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 EO6.5: 13 residues within 4Å: Chain B: H.45, F.144, N.146, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193 Ligands: EQS.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169, B:E.170 Hydrogen bonds: B:H.168, B:E.170, B:E.170, B:E.170, B:Q.193, B:Q.193 Water bridges: B:G.147, B:G.147

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain B: R.109, I.110, Q.111, P.112, F.138, Y.186 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.109, B:R.109 Salt bridges: B:R.109

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

PG4.6: 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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