SMTL ID : 4mpu.2 (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

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 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

4 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

2 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

1 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: 7 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Q.191, B:V.212, B:W.214, A:Q.87, A:Q.191, A:V.212, A:W.214 Hydrogen bonds: B:Q.87, B:G.217, B:G.217, A:Q.87, A:Q.87, A:G.217, A:G.217 Water bridges: B:Q.87, A: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptase alpha/beta-1

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