SMTL ID : 7m02.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 17c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x YL7: (1S,2S)-2-((S)-2-((((2-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid(Covalent)

YL7.1: 20 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, T.194, A.195 Ligands: YKY.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.191, A:A.195 Hydrogen bonds: A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 YL7.3: 15 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, R.192, Q.193 Ligands: YKY.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:D.191 Hydrogen bonds: B:G.147, B:S.148, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193

2 x YKY: (1R,2S)-2-((S)-2-((((2-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid(Covalent)

YKY.2: 19 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, T.194, A.195 Ligands: YL7.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.191, A:A.195 Hydrogen bonds: A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 YKY.4: 15 residues within 4Å: Chain B: H.45, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, R.192, Q.193 Ligands: YL7.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.191 Hydrogen bonds: B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193

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

PG4.5: 7 residues within 4Å: Chain B: G.19, M.21, W.35, A.74, V.77, N.99, K.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.21 Water bridges: B:G.75, B:Q.78, B:T.97

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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