SMTL ID : 7m04.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 21c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x YLV: (1R,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid(Covalent)

YLV.1: 18 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, Q.193, T.194, A.195 Ligands: YM1.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.191 Hydrogen bonds: A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147, A:G.147 YLV.3: 19 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, L.171, H.176, D.191, R.192, Q.193, T.194, A.195 Ligands: YM1.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169 Hydrogen bonds: B:F.144, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193 Water bridges: B:G.147

2 x YM1: (1S,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid(Covalent)

YM1.2: 19 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, Q.193, T.194, A.195 Ligands: YLV.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.191 Hydrogen bonds: A:F.144, A:G.147, A:C.149, A:H.168, A:E.170, A:Q.193, A:Q.193 YM1.4: 19 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, L.171, H.176, D.191, R.192, Q.193, T.194, A.195 Ligands: YLV.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169, 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, B:Q.193 Halogen bonds: B:Q.193

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

PG4.5: 9 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, V.77, L.79, N.99, K.101 3 PLIP interactions: 3 interactions with chain B Water bridges: B:M.21, B:Q.78, B:G.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies. J.Med.Chem. (2021)

Release Date

2021-03-24

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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