SMTL ID : 5wkk.1

1.55 A resolution structure of MERS 3CL protease in complex with inhibitor GC813

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

PG4.1: 6 residues within 4Å: Chain A: M.13, S.14, H.15, M.305 Chain B: Y.128, T.133 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Y.128, A:D.302, A:D.302, A:Q.306 PG4.5: 6 residues within 4Å: Chain A: Y.128, T.133 Chain B: M.13, S.14, H.15, M.305 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.302, B:Q.306

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x AW4: (1S,2S)-2-[(N-{[2-(3-chlorophenyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

AW4.3: 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, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: B3G.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.56, A:M.175, 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 AW4.7: 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, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: B3G.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.56, B:M.175, 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 B3G: (1R,2S)-2-[(N-{[2-(3-chlorophenyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

B3G.4: 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, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: AW4.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.56, A:M.175, A:Q.199 Hydrogen bonds: A:Q.174, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153, A:C.155 B3G.8: 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, A.178, H.182, D.197, Q.199, V.200, H.201 Ligands: AW4.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.56, B:M.175, B:Q.199 Hydrogen bonds: B:Q.174, B:E.176, B:E.176, B:Q.199 Water bridges: B:G.153, B:C.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galasiti Kankanamalage, A.C. et al., Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element. Eur J Med Chem (2018)

Release Date

2018-04-04

Peptides

Orf1a protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Orf1a protein

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