SMTL ID : 5mqy.1

CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

monomer

Ligands

1 x GH4: 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile(Covalent)

GH4.1: 18 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, G.61, E.63, N.66, G.67, G.68, L.69, M.70, Y.72, A.135, M.161, D.162, H.163, G.164, A.214 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.69, A:A.135, A:A.214 Hydrogen bonds: A:Q.19, A:C.25, A:H.163 Water bridges: A:C.22, A:E.63

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: K.17, N.18, F.28, E.50, E.86, Y.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18, A:N.18, A:E.86 EDO.3: 6 residues within 4Å: Chain A: D.84, S.88, Y.89, K.99, N.101, Y.104 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.101 EDO.4: 4 residues within 4Å: Chain A: A.138, G.139, D.162, W.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.162 EDO.5: 3 residues within 4Å: Chain A: S.47, E.86, E.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.87 Water bridges: A:S.47, A:S.47, A:S.47, A:S.47 EDO.6: 3 residues within 4Å: Chain A: G.81, P.102, S.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.100 Water bridges: A:S.105, A:S.105 EDO.7: 4 residues within 4Å: Chain A: V.5, D.6, W.7, K.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.6, A:D.6 EDO.8: 7 residues within 4Å: Chain A: V.54, D.55, G.58, N.62, E.63, G.64, E.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.55, A:G.58 Water bridges: A:E.63, A:E.95, A:E.95 EDO.9: 2 residues within 4Å: Chain A: K.124, T.128 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhn, B. et al., Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors. J. Med. Chem. (2017)

Release Date

2017-03-22

Peptides

Cathepsin L1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin L1

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