SMTL ID : 4mpu.1 (1 other biounit)

Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 8 residues within 4Å: Chain A: Q.82, I.88, G.89, A.90, D.177, D.178, Y.232, Y.233 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.82, A:Y.232, A:Y.232, A:Y.232 Water bridges: A:D.177, A:Y.233 Salt bridges: A:D.178 MES.5: 4 residues within 4Å: Chain B: R.173, R.176, D.177 Ligands: SO4.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.177, B:D.177 Water bridges: B:R.176, B:R.176 Salt bridges: B:R.176, B:D.177 MES.10: 8 residues within 4Å: Chain C: Q.82, I.88, G.89, A.90, D.177, D.178, Y.232, Y.233 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.82, C:D.177, C:Y.232, C:Y.232 Water bridges: C:D.177, C:Y.232 Salt bridges: C:D.178 MES.14: 4 residues within 4Å: Chain D: R.173, R.176, D.177 Ligands: SO4.17 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.177, D:D.177 Water bridges: D:R.176, D:R.176 Salt bridges: D:R.176, D:D.177

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

SO4.2: 5 residues within 4Å: Chain A: H.44, Q.191, G.192, S.194 Ligands: X2A.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.191, A:G.192, A:S.194, A:S.194, A:S.194 Salt bridges: A:H.44 SO4.6: 3 residues within 4Å: Chain B: N.184, T.185, R.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.185, B:T.185 Water bridges: B:N.222 Salt bridges: B:R.186 SO4.7: 5 residues within 4Å: Chain B: H.44, Q.191, G.192, S.194 Ligands: X2A.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.191, B:G.192, B:S.194, B:S.194, B:S.194 Water bridges: B:H.44 Salt bridges: B:H.44 SO4.8: 3 residues within 4Å: Chain B: H.156, R.173 Ligands: MES.5 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.156, B:H.156, B:D.177 Salt bridges: B:H.156, B:R.173 SO4.11: 5 residues within 4Å: Chain C: H.44, Q.191, G.192, S.194 Ligands: X2A.13 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.191, C:G.192, C:S.194, C:S.194, C:S.194 Salt bridges: C:H.44 SO4.15: 3 residues within 4Å: Chain D: N.184, T.185, R.186 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.185, D:T.185 Water bridges: D:N.222 Salt bridges: D:R.186 SO4.16: 5 residues within 4Å: Chain D: H.44, Q.191, G.192, S.194 Ligands: X2A.13 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.191, D:G.192, D:S.194, D:S.194, D:S.194 Water bridges: D:H.44 Salt bridges: D:H.44 SO4.17: 3 residues within 4Å: Chain D: H.156, R.173 Ligands: MES.14 5 PLIP interactions: 5 interactions with chain D Water bridges: D:H.156, D:H.156, D:D.177 Salt bridges: D:H.156, D:R.173

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 8 residues within 4Å: Chain A: V.20, F.28, C.45, V.50, K.51, D.52, A.55, L.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.52 PG4.9: 6 residues within 4Å: Chain B: V.20, F.28, V.50, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.52 PG4.12: 8 residues within 4Å: Chain C: V.20, F.28, C.45, V.50, K.51, D.52, A.55, L.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.52 PG4.18: 6 residues within 4Å: Chain D: V.20, F.28, V.50, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.52

2 x X2A: (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide(Non-covalent)

X2A.4: 29 residues within 4Å: Chain A: Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Chain B: Y.84, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Ligands: SO4.2, SO4.7 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Q.87, A:Q.191, A:V.212, A:W.214, B:Q.191, B:V.212, B:W.214 Hydrogen bonds: A:Q.87, A:Q.87, A:G.217, A:G.217, B:Q.87, B:G.217, B:G.217 Water bridges: A:A.86, B:Q.87 X2A.13: 29 residues within 4Å: Chain C: Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Chain D: Y.84, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Ligands: SO4.11, SO4.16 17 PLIP interactions: 10 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:Q.87, C:Q.191, C:V.212, C:W.214, D:Q.191, D:V.212, D:W.214 Hydrogen bonds: C:Q.87, C:Q.87, C:G.217, C:G.217, D:Q.87, D:Q.87, D:G.217, D:G.217 Water bridges: C:T.85, C:A.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, S.F. et al., Target-Directed Self-Assembly of Homodimeric Drugs Against beta-Tryptase. Acs Med.Chem.Lett. (2018)

Release Date

2015-03-18

Peptides

Tryptase alpha/beta-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tryptase alpha/beta-1

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