SMTL ID : 7tq8.1

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 14d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

IRK.1: 18 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, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: IUB.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.56, A:Q.199 Hydrogen bonds: A:Q.174, A:E.176, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153 IRK.4: 18 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, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: IUB.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.56, B:Q.199 Hydrogen bonds: B:Q.174, B:E.176, B:E.176, B:Q.199 Water bridges: B:G.153

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

IUB.2: 19 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, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: IRK.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.56, A:Q.199 Hydrogen bonds: A:G.153, A:S.154, A:S.154, A:C.155, A:Q.174, A:E.176, A:E.176, A:Q.199 IUB.5: 19 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, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: IRK.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.56, B:Q.199 Hydrogen bonds: B:G.153, B:S.154, B:S.154, B:C.155, B:Q.174, B:E.176, B:E.176, B:Q.199

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

PG4.3: 5 residues within 4Å: Chain A: M.13, H.15, M.305 Chain B: T.133, L.151 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:M.13, A:H.15, A:H.15, A:T.137, A:D.302, B:T.133 PG4.6: 5 residues within 4Å: Chain A: T.133, L.151 Chain B: M.13, H.15, M.305 4 PLIP interactions: 4 interactions with chain B Water bridges: B:M.13, B:H.15, B:H.15, B:T.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies. Acs Pharmacol Transl Sci (2023)

Release Date

2022-03-02

Peptides

Orf1a protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Orf1a protein

Related Entries With Identical Sequence