SMTL ID : 4ym9.1

Crystal structure of Porcine Pancreatic Elastase (PPE) in complex with the novel inhibitor JM102

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 4E4: 2-ethyl-2-(hydroxymethyl)-N-(6-methylpyridin-3-yl)butanamide(Covalent)

4E4.1: 13 residues within 4Å: Chain A: H.45, T.85, V.88, C.184, Q.185, G.186, D.187, S.188, T.206, S.207, F.208, V.209 Ligands: SO4.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.185, A:T.206, A:V.209, A:V.209 Hydrogen bonds: A:G.186, A:D.187, A:S.188, A:S.207 pi-Stacking: A:H.45

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: W.12, Y.128, Q.147, Y.200 Ligands: ACT.7, ACT.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.147 SO4.3: 7 residues within 4Å: Chain A: A.117, G.118, S.227, A.228, Y.229, I.230, S.231 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.118, A:I.230, A:S.231, A:S.231 Water bridges: A:A.228, A:A.228, A:W.232 SO4.4: 5 residues within 4Å: Chain A: F.208, V.209, S.210 Ligands: 4E4.1, SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.209 SO4.5: 6 residues within 4Å: Chain A: V.88, W.164, T.167, F.208, V.209 Ligands: SO4.4 No protein-ligand interaction detected (PLIP) SO4.6: 7 residues within 4Å: Chain A: T.137, Q.185, S.210, R.211, L.212, G.213, C.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.185

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain A: Y.128, Y.149 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.128 Water bridges: A:Y.149 ACT.8: 2 residues within 4Å: Chain A: S.166, T.167 No protein-ligand interaction detected (PLIP) ACT.9: 4 residues within 4Å: Chain A: W.26, R.54, Y.71, V.72 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.71 Salt bridges: A:R.54 ACT.10: 4 residues within 4Å: Chain A: S.11, W.12, Y.200 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.12, A:Y.200 ACT.11: 4 residues within 4Å: Chain A: A.142, Q.143, T.144, Q.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.143, A:T.144, A:T.144 Water bridges: A:Q.146

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 5 residues within 4Å: Chain A: E.59, N.61, Q.64, N.65, E.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.61, A:Q.64, A:D.66 Water bridges: A:H.60

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: Q.19, W.26, A.27, H.28, L.62, N.63 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.28, A:L.62, A:N.63 Water bridges: A:Q.19, A:Q.19, A:H.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruivo, E.F. et al., Clickable 4-Oxo-beta-lactam-Based Selective Probing for Human Neutrophil Elastase Related Proteomes. ChemMedChem (2016)

Release Date

2016-06-29

Peptides

Chymotrypsin-like elastase family member 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chymotrypsin-like elastase family member 1

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