SMTL ID : 6jkf.1

Crystal structure of Serratia marcescens Chitinase B complexed with compound 2-8-s2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

3 x BV0: 6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide(Non-covalent)

BV0.1: 13 residues within 4Å: Chain A: F.49, W.95, E.142, M.210, D.213, W.218, Y.290, G.312, E.313, D.314, R.336, W.401 Chain B: Y.479 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.218, A:W.218, A:D.314, B:Y.479, B:Y.479 Hydrogen bonds: A:W.95, A:D.213, A:D.213 Water bridges: A:R.292 pi-Stacking: A:W.95, A:W.95, A:W.95, A:W.218, A:W.218, A:W.218, A:W.401, A:W.401 pi-Cation interactions: A:R.292 BV0.2: 13 residues within 4Å: Chain A: Y.479 Chain B: Y.8, F.49, W.95, D.140, E.142, F.189, M.210, Y.212, D.213, D.314, W.401 Ligands: BV0.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.49, B:W.95, B:W.401, A:Y.479 Hydrogen bonds: B:W.95, B:D.213 pi-Stacking: B:W.95, B:W.95, B:W.95, B:W.95, B:W.401 BV0.3: 11 residues within 4Å: Chain A: T.459, Y.460, A.461, G.478, Y.479 Chain B: F.188, F.189, D.213, W.218, R.292 Ligands: BV0.2 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.188, B:F.189, B:D.213, B:W.218, A:A.461, A:Y.479 Water bridges: B:E.219, A:G.478, A:G.478 pi-Stacking: B:W.218, B:W.218, B:W.218, B:W.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, X. et al., A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors. J.Med.Chem. (2020)

Release Date

2020-02-19

Peptides

Chitinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chitinase