SMTL ID : 9qfu.1

Human Tryptase beta-2 (hTPSB2) complexed with covalent inhibitor Compound #1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

4 x 01: ~{N}-[(1~{S},2~{S})-6-azanyl-1-[5-[[4-[2-(3,4-dichlorophenyl)ethoxy]phenyl]methyl]-1,2,4-oxadiazol-3-yl]-1-oxidanyl-hexan-2-yl]-4-fluoranyl-benzamide

01.1: 24 residues within 4Å: Chain A: V.20, F.28, H.44, C.45, V.46, K.51, D.52, A.55, L.56, A.86, Q.87, D.188, S.189, C.190, Q.191, G.192, D.193, S.194, V.212, S.213, W.214, G.215, G.217, G.225 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.20, A:F.28, A:F.28, A:A.86, A:W.214 Hydrogen bonds: A:S.189, A:Q.191, A:G.192, A:D.193, A:S.194, A:S.213 Water bridges: A:I.226 pi-Stacking: A:H.44 Halogen bonds: A:D.52 01.11: 23 residues within 4Å: Chain B: V.20, F.28, H.44, C.45, V.46, K.51, D.52, A.55, L.56, A.86, Q.87, D.188, S.189, C.190, Q.191, G.192, D.193, S.194, V.212, S.213, W.214, G.217, G.225 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.20, B:F.28, B:K.51, B:A.86, B:W.214 Hydrogen bonds: B:D.188, B:G.192, B:D.193, B:S.194, B:S.213 Water bridges: B:I.226 pi-Stacking: B:H.44 Halogen bonds: B:D.52 01.20: 24 residues within 4Å: Chain C: V.20, F.28, H.44, C.45, V.46, K.51, D.52, A.55, L.56, A.86, Q.87, D.188, S.189, C.190, Q.191, G.192, D.193, S.194, V.212, S.213, W.214, G.215, G.217, G.225 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.20, C:K.51, C:A.86, C:W.214 Hydrogen bonds: C:S.189, C:Q.191, C:G.192, C:D.193, C:S.194, C:S.213 Water bridges: C:I.226 pi-Stacking: C:H.44 Halogen bonds: C:D.52 01.32: 22 residues within 4Å: Chain D: V.20, F.28, H.44, C.45, V.46, K.51, D.52, L.56, A.86, Q.87, D.188, S.189, C.190, Q.191, G.192, D.193, S.194, V.212, S.213, W.214, G.217, G.225 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.20, D:F.28, D:F.28, D:A.86, D:V.212, D:W.214 Hydrogen bonds: D:S.189, D:Q.191, D:G.192, D:D.193, D:S.194, D:S.213 Water bridges: D:I.226 pi-Stacking: D:H.44 Halogen bonds: D:D.52

16 x SO4: SULFATE ION

SO4.2: 3 residues within 4Å: Chain A: N.184, R.186, R.187 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: H.239 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: K.11, K.201, W.206 Ligands: EDO.7 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: R.9, Q.63, H.64, Q.68 Chain B: Y.67 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: N.184, R.186, R.187 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: K.11, K.201, W.206 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: R.76, H.239, Y.240 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: N.184, R.186, R.187 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: K.11, K.201, W.206 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain C: N.184, T.185 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: S.104, S.105 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain C: R.9, E.62, Q.63, H.64, Q.68 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: N.184, R.186, R.187 Ligand excluded by PLIP SO4.34: 1 residues within 4Å: Chain D: H.239 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain D: K.11, K.201, W.206 Ligands: EDO.38 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain C: Y.67 Chain D: R.9, Q.63, H.64, Q.68 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER

PEG.6: 5 residues within 4Å: Chain A: Q.82, I.88, D.178, Y.233 Chain C: V.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.82, A:Y.233 PEG.39: 3 residues within 4Å: Chain D: Q.82, I.88, Y.233 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.82, D:D.178

15 x EDO: 1,2-ETHANEDIOL

EDO.7: 5 residues within 4Å: Chain A: K.11, W.12, W.126, W.206 Ligands: SO4.4 No protein-ligand interaction detected (PLIP) EDO.8: 1 residues within 4Å: Chain A: D.170 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: N.155, D.177, R.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.177 Water bridges: A:R.173, A:R.229 EDO.16: 3 residues within 4Å: Chain B: K.11, W.12, W.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.147 EDO.18: 4 residues within 4Å: Chain B: L.164, P.221, N.222, R.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.222 Water bridges: B:R.223 EDO.19: 1 residues within 4Å: Chain B: Y.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.232 EDO.25: 4 residues within 4Å: Chain C: K.11, W.12, W.126, Q.147 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.147 EDO.28: 3 residues within 4Å: Chain C: S.10, S.105, H.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.106 EDO.29: 4 residues within 4Å: Chain C: L.164, P.221, N.222, R.223 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.222, C:R.223 Water bridges: C:P.221, C:R.223, A:D.49 EDO.30: 4 residues within 4Å: Chain A: P.48, Y.84 Chain C: Q.87, E.216 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.87, C:E.216, C:E.216 Water bridges: A:Y.84 EDO.31: 2 residues within 4Å: Chain C: R.76, Y.240 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.76, C:R.76 Water bridges: C:Y.240 EDO.35: 6 residues within 4Å: Chain D: Q.5, W.126, Q.147, V.148, K.149, R.187 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.5, D:Q.147, D:K.149, D:R.187 Water bridges: D:R.187 EDO.38: 5 residues within 4Å: Chain D: K.11, W.12, W.126, Q.147 Ligands: SO4.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.147 EDO.40: 2 residues within 4Å: Chain D: D.170, D.171 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.171 EDO.41: 3 residues within 4Å: Chain D: N.184, T.185, R.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.185, D:R.186

3 x ACT: ACETATE ION

ACT.10: 7 residues within 4Å: Chain A: G.4, Q.5, W.126, Q.147, V.148, K.149, R.187 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.126 Hydrogen bonds: A:Q.5, A:Q.147, A:K.149 Water bridges: A:R.187 Salt bridges: A:R.187 ACT.14: 2 residues within 4Å: Chain B: H.108, W.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.108, B:W.206 ACT.26: 1 residues within 4Å: Chain C: H.156 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.156 Salt bridges: C:H.156, C:R.173

1 x GOL: GLYCEROL

GOL.15: 5 residues within 4Å: Chain B: R.9, E.62, Q.63, H.64, Y.67 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.9, B:R.9, B:Q.63, B:H.64, B:H.64 Water bridges: B:R.61, B:H.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porta, A. et al., Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors. Molecules (2025)

Release Date

2025-03-26

Peptides

Tryptase beta-2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptase beta-2

Related Entries With Identical Sequence