SMTL ID : 8e6b.1

Crystal structure of MERS 3CL protease in complex with a dimethyl sulfinyl benzene inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x URR: N~2~-(ethoxycarbonyl)-N-{(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide(Covalent)

URR.1: 21 residues within 4Å: Chain A: H.48, L.56, 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: UO9.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.56 Hydrogen bonds: A:F.150, A:G.153, A:S.154, A:S.154, A:C.155, A:Q.174, A:E.176, A:E.176, A:Q.199, A:Q.199, A:Q.202 URR.3: 22 residues within 4Å: Chain B: H.48, L.56, 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, K.198, Q.199, V.200, H.201, Q.202 Ligands: UO9.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:H.48, B:L.56, B:A.178 Hydrogen bonds: B:F.150, B:G.153, B:S.154, B:S.154, B:C.155, B:Q.174, B:E.176, B:Q.199, B:Q.199, B:Q.202 pi-Stacking: B:H.201 pi-Cation interactions: B:H.201

2 x UO9: (2~{S})-2-[[(2~{S})-4-methyl-2-[[2-methyl-2-[oxidanyl(phenyl)-$l^{3}-sulfanyl]propoxy]carbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

UO9.2: 21 residues within 4Å: Chain A: H.48, L.56, 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, K.198, Q.199, V.200, H.201, Q.202 Ligands: URR.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.56, A:M.175 Hydrogen bonds: A:Q.174, A:E.176, A:E.176, A:E.176, A:Q.199, A:Q.199, A:Q.202 Water bridges: A:G.153 UO9.4: 21 residues within 4Å: Chain B: H.48, L.56, 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, K.198, Q.199, V.200, H.201, Q.202 Ligands: URR.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.48, B:L.56, B:A.178 Hydrogen bonds: B:S.154, B:Q.174, B:E.176, B:E.176, B:Q.199, B:Q.199, B:Q.202 Water bridges: B:G.153 pi-Stacking: B:H.201

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
B

Orf1a protein

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