SMTL ID : 7lzt.1

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 8b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: H.68, N.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.69, A:N.69 Water bridges: A:S.66, A:H.68 Salt bridges: A:H.68 SO4.4: 2 residues within 4Å: Chain B: H.68, N.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.69, B:N.69 Water bridges: B:S.66, B:H.68 Salt bridges: B:H.68

2 x YMY: (1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)methoxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid(Covalent)

YMY.2: 18 residues within 4Å: Chain A: H.45, Y.58, 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: YN1.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.45, A:M.169, A:P.172, A:Q.193 Hydrogen bonds: A:H.168, A:E.170, A:E.170, A:Q.193 Water bridges: A:G.147 YMY.5: 18 residues within 4Å: Chain B: H.45, Y.58, 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: YN1.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169, B:P.172, B:Q.193 Hydrogen bonds: B:H.168, B:E.170, B:E.170, B:E.170, B:Q.193 Water bridges: B:G.147

2 x YN1: (1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)methoxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid(Covalent)

YN1.3: 18 residues within 4Å: Chain A: H.45, M.53, Y.58, F.144, 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: YMY.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:P.172, A:D.191, A:Q.193 Hydrogen bonds: A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193 YN1.6: 18 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, 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: YMY.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.45, B:P.172, B:D.191, B:Q.193 Hydrogen bonds: B:G.147, B:S.148, B:C.149, 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 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
A

3C-like proteinase

Related Entries With Identical Sequence