SMTL ID : 5wkj.1

2.05 A resolution structure of MERS 3CL protease in complex with inhibitor GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.2: 1 residues within 4Å: Chain A: T.108 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.108, H2O.4, H2O.5, H2O.6, H2O.7 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain B: T.108 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.108, H2O.11, H2O.12, H2O.13, H2O.14

2 x B1S: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

B1S.3: 16 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 Ligands: K36.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.48 Hydrogen bonds: A:F.150, A:Q.174, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153 B1S.7: 16 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 Ligands: K36.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.48 Hydrogen bonds: B:F.150, B:Q.174, B:E.176, B:Q.199 Water bridges: B:G.153

2 x K36: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

K36.4: 17 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 Ligands: B1S.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.48 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 K36.8: 17 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 Ligands: B1S.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.48 Hydrogen bonds: B:F.150, B:G.153, B:S.154, B:C.155, B:Q.174, B:E.176, B:Q.199

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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