SMTL ID : 5a0b.1

Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 9 residues within 4Å: Chain A: W.12, Q.121, C.122, N.144, V.178, C.179, N.180, G.181 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.12, A:V.178 Hydrogen bonds: A:Q.121, A:N.180, A:G.181, A:Q.121, A:N.144 NAG-FUC.2: 7 residues within 4Å: Chain A: R.49, A.50, V.51, R.52, V.69, A.71, N.95 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.52, A:A.71 Hydrogen bonds: A:R.52, A:A.71 Water bridges: A:N.95, A:N.95

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.3: 2 residues within 4Å: Ligands: NAG-FUC.1, NAG-FUC.1 No protein-ligand interaction detected (PLIP)

1 x JJX: (4R)-4-(4-cyanophenyl)-6-methyl-2-oxidanylidene-3-[2-oxidanylidene-2-(4-propan-2-ylpiperazin-1-yl)ethyl]-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidine-5-carbonitrile(Non-covalent)

JJX.4: 16 residues within 4Å: Chain A: H.41, Y.80, D.81, P.82, L.85, D.88, V.168, C.169, F.170, D.172, S.173, A.187, S.188, F.189, V.190 Ligands: DMS.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.41, A:L.85, A:F.170, A:F.189, A:V.190, A:V.190 Hydrogen bonds: A:V.190

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

DMS.5: 6 residues within 4Å: Chain A: F.170, V.190, R.191, G.192, G.193 Ligands: JJX.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

von Nussbaum, F. et al., Freezing the Bioactive Conformation to Boost Potency: The Identification of BAY 85-8501, a Selective and Potent Inhibitor of Human Neutrophil Elastase for Pulmonary Diseases. ChemMedChem (2015)

Release Date

2015-08-19

Peptides

NEUTROPHIL ELASTASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NEUTROPHIL ELASTASE

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