SMTL ID : 7c92.1

Structure of Serratia marcescens chitinase B complexed with compound 6k

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

3 x FXR: 6-azanyl-11-methyl-2-oxidanylidene-N-(pyridin-3-ylmethyl)-1,7,9-triazatricyclo[8.4.0.0^3,8]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide(Non-covalent)

FXR.1: 10 residues within 4Å: Chain A: Y.14, F.55, W.101, D.146, E.148, M.216, Y.218, D.219, W.224, W.407 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.101, A:W.407 Hydrogen bonds: A:D.219, A:D.219 pi-Stacking: A:Y.14, A:W.101, A:W.101, A:W.101, A:W.101, A:W.224, A:W.224, A:W.224 FXR.2: 12 residues within 4Å: Chain A: Y.485 Chain B: Y.14, F.55, W.101, D.146, E.148, F.195, M.216, Y.218, D.219, W.407 Ligands: FXR.3 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.101, B:F.195, B:W.407, A:Y.485 Hydrogen bonds: B:D.219 Water bridges: B:W.101 pi-Stacking: B:Y.14, B:W.101, B:W.101, B:W.101, B:W.101, B:W.407 FXR.3: 9 residues within 4Å: Chain A: Y.466, A.467, Q.468, G.484, Y.485 Chain B: D.219, W.224, R.298 Ligands: FXR.2 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.219, B:W.224, B:W.224 Hydrogen bonds: B:E.225, A:Y.485 Water bridges: B:E.225, A:G.484 pi-Stacking: B:W.224, B:W.224, B:W.224, B:W.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2021-06-09

Peptides

Chitinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chitinase