SMTL ID : 8e6e.1

Crystal structure of MERS 3CL protease in complex with a phenyl sulfane inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x UUR: 2-phenylsulfanylethyl ~{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)

UUR.1: 20 residues within 4Å: Chain A: H.48, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, Q.199, V.200, H.201, Q.202 Ligands: UV2.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.48, A:L.177, A:Q.202 Hydrogen bonds: A:F.150, A:G.153, A:S.154, A:C.155, A:Q.174, A:E.176, A:E.176, A:Q.199 UUR.3: 20 residues within 4Å: Chain B: H.48, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, Q.199, V.200, H.201, Q.202 Ligands: UV2.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.48, B:L.177, B:Q.202 Hydrogen bonds: B:F.150, B:G.153, B:S.154, B:C.155, B:Q.174, B:E.176, B:Q.199

2 x UV2: (1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-[(N-{[2-(phenylsulfanyl)ethoxy]carbonyl}-L-leucyl)amino]propane-1-sulfonic acid(Covalent)

UV2.2: 19 residues within 4Å: Chain A: H.48, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, Q.199, V.200, H.201, Q.202 Ligands: UUR.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.48, A:L.177, A:Q.202 Hydrogen bonds: A:F.150, A:S.154, A:Q.174, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153 UV2.4: 19 residues within 4Å: Chain B: H.48, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, Q.199, V.200, H.201, Q.202 Ligands: UUR.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.48, B:L.177, B:Q.202 Hydrogen bonds: B:F.150, B:S.154, B:Q.174, B:E.176, B:Q.199 Water bridges: B:G.153

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

2022-09-07

Peptides

Orf1a protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Orf1a protein

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