SMTL ID : 8f45.1

Crystal structure of SARS-CoV-2 3CL protease in complex with a phenyl dimethyl sulfane inhibitor (cyclopropyl ketoamide warhead)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x XF8: (2-methyl-2-phenylsulfanyl-propyl) ~{N}-[(2~{S})-1-[[(2~{S},3~{S})-3-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate(Covalent)

XF8.1: 21 residues within 4Å: Chain A: T.30, H.45, M.53, 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, Q.196 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.191 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:Q.193, A:Q.193 XF8.2: 22 residues within 4Å: Chain B: T.30, L.31, H.45, M.53, 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.31, 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

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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