SMTL ID : 5nh0.1

Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-Butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)b- utan-2-yl)carbamate (tert-butyl -GlnLactam-CO-CO-NH-benzyl)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

6 x 8X8: ~{tert}-butyl ~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]carbamate(Covalent)

8X8.1: 16 residues within 4Å: Chain A: V.26, H.41, T.47, F.139, N.141, G.142, A.143, C.144, H.163, Q.164, I.165, E.166, H.172, D.187, Q.188, P.189 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.47, A:N.141, A:I.165 Hydrogen bonds: A:F.139, A:G.142, A:C.144, A:Q.164 Water bridges: A:E.166 8X8.4: 16 residues within 4Å: Chain B: V.26, H.41, T.47, F.139, I.140, N.141, G.142, A.143, C.144, H.163, Q.164, I.165, E.166, D.187, Q.188, P.189 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.47, B:N.141, B:I.165 Hydrogen bonds: B:F.139, B:G.142, B:C.144, B:Q.164 8X8.5: 16 residues within 4Å: Chain C: V.26, H.41, T.47, F.139, I.140, N.141, G.142, A.143, C.144, H.163, Q.164, E.166, H.172, D.187, Q.188, P.189 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.47, C:N.141 Hydrogen bonds: C:G.142, C:A.143, C:C.144, C:Q.164 8X8.9: 16 residues within 4Å: Chain D: V.26, H.41, T.47, F.139, N.141, G.142, A.143, C.144, H.163, Q.164, I.165, E.166, H.172, D.187, Q.188, P.189 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:T.47, D:N.141, D:I.165 Hydrogen bonds: D:F.139, D:G.142, D:C.144, D:Q.164, D:E.166 Water bridges: D:E.166 8X8.12: 16 residues within 4Å: Chain E: V.26, H.41, T.47, F.139, I.140, N.141, G.142, A.143, C.144, H.163, Q.164, I.165, E.166, D.187, Q.188, P.189 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:T.47, E:N.141, E:I.165 Hydrogen bonds: E:F.139, E:G.142, E:C.144, E:Q.164 8X8.13: 16 residues within 4Å: Chain F: V.26, H.41, T.47, F.139, I.140, N.141, G.142, A.143, C.144, H.163, Q.164, E.166, H.172, D.187, Q.188, P.189 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:T.47, F:N.141 Hydrogen bonds: F:G.142, F:A.143, F:C.144, F:Q.164, F:E.166

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: D.202, C.247, Y.248, L.290 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.290 Salt bridges: A:D.202 DMS.3: 2 residues within 4Å: Chain A: R.130, K.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130, A:R.130 DMS.8: 1 residues within 4Å: Chain C: R.130 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.130 DMS.10: 4 residues within 4Å: Chain D: D.202, C.247, Y.248, L.290 2 PLIP interactions: 2 interactions with chain D Water bridges: D:L.290 Salt bridges: D:D.202 DMS.11: 2 residues within 4Å: Chain D: R.130, K.136 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.130, D:R.130 DMS.16: 1 residues within 4Å: Chain F: R.130 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.130

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain B: Y.117, S.122 Chain C: M.6, K.295, Q.296 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.295, C:K.295, B:S.122 Water bridges: C:Q.296, B:Y.117, B:S.122 GOL.7: 10 residues within 4Å: Chain C: K.5, M.6, Q.8, S.110, F.111, N.112, G.126, N.150, E.292, K.295 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.111, C:N.150, C:K.295, C:K.295 Water bridges: C:M.6 GOL.14: 5 residues within 4Å: Chain E: Y.117, S.122 Chain F: M.6, K.295, Q.296 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:S.122, F:K.295, F:K.295 Water bridges: E:S.122, F:Q.296 GOL.15: 10 residues within 4Å: Chain F: K.5, M.6, Q.8, S.110, F.111, N.112, G.126, N.150, E.292, K.295 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:F.111, F:N.150, F:E.292, F:K.295, F:K.295 Water bridges: F:M.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, D. et al., Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication. To Be Published

Release Date

2018-05-16

Peptides

3C-like proteinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

3C-like proteinase