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

Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: K.11, W.12, P.13, W.14, W.206 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: K.11, W.12, P.13, W.14 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: K.11, W.12, P.13, W.14, W.206 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: K.11, W.12, P.13, W.14 Ligand excluded by PLIP

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: V.20, F.28, K.51, D.52, A.55, L.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.52 PGE.7: 6 residues within 4Å: Chain B: V.20, F.28, C.45, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.52 PGE.9: 6 residues within 4Å: Chain C: V.20, F.28, K.51, D.52, A.55, L.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.52 PGE.14: 6 residues within 4Å: Chain D: V.20, F.28, C.45, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.52

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: F.28, H.44, Q.191, G.192, S.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.192, A:S.194, A:S.194 Salt bridges: A:H.44 ACT.5: 5 residues within 4Å: Chain B: F.28, H.44, Q.191, G.192, S.194 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Q.191 Hydrogen bonds: B:G.192, B:S.194, B:S.194 Water bridges: B:H.44, B:Q.191, B:Q.191 Salt bridges: B:H.44 ACT.10: 5 residues within 4Å: Chain C: F.28, H.44, Q.191, G.192, S.194 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.192, C:S.194, C:S.194 Salt bridges: C:H.44 ACT.12: 5 residues within 4Å: Chain D: F.28, H.44, Q.191, G.192, S.194 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Q.191 Hydrogen bonds: D:G.192, D:S.194, D:S.194 Water bridges: D:H.44, D:Q.191, D:Q.191 Salt bridges: D:H.44

2 x 2AJ: [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)(Non-covalent)

2AJ.4: 28 residues within 4Å: Chain A: T.85, 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: T.85, 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 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.212, B:W.214, A:V.212, A:W.214 Hydrogen bonds: B:G.217, B:G.217, A:G.217, A:G.217 2AJ.11: 28 residues within 4Å: Chain C: T.85, 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: T.85, 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 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.212, D:W.214, C:V.212, C:W.214 Hydrogen bonds: D:G.217, D:G.217, C:G.217, C:G.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, S.F. et al., A Novel, Nonpeptidic, Orally Active Bivalent Inhibitor of Human beta-Tryptase. Pharmacology (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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