SMTL ID : 7cb1.1

Structure of Serratia marcescens chitinase B complexed with compound 6q

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

3 x FO0: 6-azanyl-11-methyl-2-oxidanylidene-N-[(1S)-1-pyridin-3-ylethyl]-1,7,9-triazatricyclo[8.4.0.0^{3,8}]tetradeca-3,5,7,9,11,13-hexaene-5-carboxamide(Non-covalent)

FO0.1: 12 residues within 4Å: Chain A: Y.14, F.55, W.101, D.146, E.148, F.195, M.216, Y.218, D.219, W.407 Chain B: Y.485 Ligands: FO0.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.55, A:W.101, A:W.101, A:W.101, A:F.195, A:Y.218, B:Y.485, B:Y.485 Hydrogen bonds: A:D.219 Water bridges: A:W.101, A:D.320 pi-Stacking: A:W.101, A:W.101, A:W.101, A:W.407 FO0.2: 7 residues within 4Å: Chain A: D.219, W.224, R.298, G.318 Chain B: G.484, Y.485 Ligands: FO0.1 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.485, A:W.224 Hydrogen bonds: B:G.484 Water bridges: B:G.484, A:G.318 pi-Stacking: A:W.224, A:W.224, A:W.224, A:W.224 FO0.3: 10 residues within 4Å: Chain A: Y.485 Chain B: F.55, W.101, E.148, F.195, M.216, Y.218, D.219, Y.296, W.407 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:Y.485, B:F.55, B:W.101, B:W.101, B:W.101, B:F.195, B:Y.218 Hydrogen bonds: B:W.101, B:D.219 Water bridges: B:R.298, B:R.298 pi-Stacking: B:W.101, B:W.101, B:W.101, B:W.224, B:W.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, X. et al., Discovery of novel Chitinase Inhibitors with a scaffold of dipyridopyrimidine-3-carboxamide via Structure-based Rational Design. To Be Published

Release Date

2021-06-16

Peptides

Chitinase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chitinase B