SMTL ID : 8f44.1

Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl phenyl sulfane inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x XFF: (2-methyl-2-phenylsulfanyl-propyl) ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate(Covalent)

XFF.1: 19 residues within 4Å: Chain A: H.45, M.53, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, Q.193, T.194, A.195 Ligands: XFR.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.172, A:P.172 Hydrogen bonds: A:G.147, A:S.148, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 XFF.3: 20 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, P.172, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: XFR.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:F.144, B:G.147, B:S.148, B:S.148, B:C.149, B:H.168, B:E.170, B:Q.193, B:Q.193

2 x XFR: (1R,2S)-1-hydroxy-2-[(N-{[2-methyl-2-(phenylsulfanyl)propoxy]carbonyl}-L-leucyl)amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

XFR.2: 19 residues within 4Å: Chain A: H.45, M.53, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, R.192, Q.193, T.194, A.195 Ligands: XFF.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:P.172, A:D.191, A:A.195 Hydrogen bonds: A:S.148, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147 XFR.4: 19 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, L.171, P.172, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: XFF.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:P.172, B:D.191, B:Q.196 Hydrogen bonds: B:F.144, B:S.148, B:H.168, B:E.170, B:Q.193, B:Q.193 Water bridges: B:G.147

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

PG4.5: 8 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, V.77, L.79, N.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.101 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 direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem. (2023)

Release Date

2022-11-23

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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