SMTL ID : 8r4x.2 (3 other biounits)

Structure of Chitinase-3-like protein 1 in complex with inhibitor 30

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

1 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: 6 residues within 4Å: Chain A: N.60, I.61, S.62, T.68, W.69, R.105 No protein-ligand interaction detected (PLIP)

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: Y.141, S.179, T.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.179 Water bridges: A:S.179, A:S.179, A:A.180 EDO.3: 5 residues within 4Å: Chain A: W.31, F.58, G.98, W.99, N.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.99, A:N.100, A:N.100 EDO.4: 2 residues within 4Å: Chain A: R.117, K.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.117 EDO.5: 5 residues within 4Å: Chain A: Y.22, L.24, T.52, K.377, L.380 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.50

1 x XZ0: (2~{S},5~{S})-4-[1-(4-chloranylpyridin-2-yl)piperidin-4-yl]-5-[(4-chlorophenyl)methyl]-2-methyl-morpholine(Non-covalent)

XZ0.6: 19 residues within 4Å: Chain A: Y.27, F.58, W.99, A.138, L.140, A.177, M.204, Y.206, D.207, F.261, R.263, T.288, E.290, T.293, L.294, A.295, M.350, W.352, L.356 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.99, A:L.140, A:A.177, A:Y.206, A:F.261, A:F.261, A:T.293, A:W.352, A:W.352, A:L.356 Hydrogen bonds: A:Y.206 Salt bridges: A:D.207 pi-Stacking: A:Y.27 pi-Cation interactions: A:W.99, A:W.99

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

CL.7: 1 residues within 4Å: Chain A: E.227 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.233, Y.239, R.246 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czestkowski, W. et al., Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J.Med.Chem. (2024)

Release Date

2024-03-13

Peptides

Chitinase-3-like protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Chitinase-3-like protein 1

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