SMTL ID : 3pdf.1

Discovery of Novel Cyanamide-Based Inhibitors of Cathepsin C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: H.217, I.219, N.252 Chain B: L.54 Chain D: F.206, L.207, T.209 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.219 NAG-NAG.6: 7 residues within 4Å: Chain A: L.54 Chain B: H.217, I.219, N.252 Chain C: F.206, L.207, T.209 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.219 NAG-NAG.11: 7 residues within 4Å: Chain B: F.206, L.207, T.209 Chain C: H.217, I.219, N.252 Chain D: L.54 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.219 NAG-NAG.16: 7 residues within 4Å: Chain A: F.206, L.207, T.209 Chain C: L.54 Chain D: H.217, I.219, N.252 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.219

4 x LXV: 2,5-dibromo-N-{(3R,5S)-1-[(Z)-iminomethyl]-5-methylpyrrolidin-3-yl}benzenesulfonamide(Covalent)

LXV.2: 14 residues within 4Å: Chain A: D.1, Y.64, Q.228, G.232, S.233, C.234, G.276, G.277, F.278, P.279, A.349, T.379, N.380, A.382 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.64 Hydrogen bonds: A:D.1, A:Q.228, A:C.234, A:G.277 Water bridges: A:D.1, A:C.231, A:H.381 pi-Stacking: A:F.278 Halogen bonds: A:D.1 LXV.7: 14 residues within 4Å: Chain B: D.1, Y.64, Q.228, G.232, S.233, C.234, G.276, G.277, F.278, P.279, A.349, T.379, N.380, A.382 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.64 Hydrogen bonds: B:D.1, B:Q.228, B:C.234, B:G.277 Water bridges: B:D.1, B:C.231, B:H.381 pi-Stacking: B:F.278 Halogen bonds: B:D.1 LXV.12: 14 residues within 4Å: Chain C: D.1, Y.64, Q.228, G.232, S.233, C.234, G.276, G.277, F.278, P.279, A.349, T.379, N.380, A.382 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.64 Hydrogen bonds: C:D.1, C:Q.228, C:C.234, C:G.277 Water bridges: C:C.231 pi-Stacking: C:F.278 Halogen bonds: C:D.1 LXV.17: 14 residues within 4Å: Chain D: D.1, Y.64, Q.228, G.232, S.233, C.234, G.276, G.277, F.278, P.279, A.349, T.379, N.380, A.382 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.64 Hydrogen bonds: D:D.1, D:Q.228, D:C.234, D:G.277 Water bridges: D:C.231 pi-Stacking: D:F.278 Halogen bonds: D:D.1

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.95 NAG.4: 4 residues within 4Å: Chain A: N.5, N.65, F.376, L.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 NAG.8: 1 residues within 4Å: Chain B: N.95 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.95 NAG.9: 4 residues within 4Å: Chain B: N.5, N.65, F.376, L.378 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.65 NAG.13: 1 residues within 4Å: Chain C: N.95 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.95 NAG.14: 4 residues within 4Å: Chain C: N.5, N.65, F.376, L.378 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.65 NAG.18: 1 residues within 4Å: Chain D: N.95 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.95 NAG.19: 4 residues within 4Å: Chain D: N.5, N.65, F.376, L.378 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.65

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: F.278, P.279, Y.280, Y.323, V.431 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: F.278, P.279, Y.280, Y.323, V.431 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: F.278, P.279, Y.280, Y.323, V.431 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: F.278, P.279, Y.280, Y.323, V.431 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laine, D. et al., Discovery of novel cyanamide-based inhibitors of cathepsin C. Acs Med.Chem.Lett. (2011)

Release Date

2011-10-26

Peptides

Dipeptidyl peptidase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Dipeptidyl peptidase 1