SMTL ID : 8r42.1

Structure of CHI3L1 in complex with inhibititor 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

2 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) NAG-NAG.2: 7 residues within 4Å: Chain B: N.60, I.61, S.62, N.63, T.68, W.69, R.105 No protein-ligand interaction detected (PLIP)

2 x XUC: 2-[4-[(2~{R})-2-[(4-chlorophenyl)methyl]pyrrolidin-1-yl]piperidin-1-yl]pyridine(Non-covalent)

XUC.3: 18 residues within 4Å: Chain A: Y.27, F.58, W.99, L.140, A.177, M.204, Y.206, D.207, F.261, R.263, T.288, E.290, T.293, L.294, A.295, W.352, L.356 Ligands: EDO.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.99, A:A.177, A:F.261, A:F.261, A:L.356 Salt bridges: A:D.207 pi-Stacking: A:Y.27, A:W.352 pi-Cation interactions: A:W.99 XUC.15: 16 residues within 4Å: Chain B: Y.27, W.99, L.140, A.177, M.204, Y.206, D.207, F.261, R.263, T.288, E.290, T.293, L.294, A.295, W.352, L.356 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.99, B:A.177, B:F.261, B:T.293, B:L.356 Salt bridges: B:D.207 pi-Stacking: B:Y.27, B:F.261, B:W.352 pi-Cation interactions: B:W.99

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

EDO.4: 3 residues within 4Å: Chain A: H.65, S.122, P.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.65 EDO.5: 5 residues within 4Å: Chain A: W.31, R.35, W.99, E.290 Ligands: XUC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.35 EDO.6: 2 residues within 4Å: Chain A: K.23, H.53 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain A: R.117, K.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.117 EDO.8: 3 residues within 4Å: Chain A: K.158, Q.196, H.197 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.197 EDO.9: 3 residues within 4Å: Chain A: D.67, T.68, V.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.68 EDO.10: 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.11: 3 residues within 4Å: Chain A: D.207, H.209, R.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.207, A:R.263, A:R.263 EDO.12: 4 residues within 4Å: Chain A: T.266, L.267, S.279, N.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.267, A:S.279 EDO.16: 2 residues within 4Å: Chain B: R.233 Ligands: SO4.13 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 4 residues within 4Å: Chain A: R.233 Chain B: R.224, E.227 Ligands: EDO.16 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.233, B:R.224 Hydrogen bonds: B:E.227 Water bridges: B:R.233

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

CL.14: 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chitinase-3-like protein 1

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