SMTL ID : 1y5u.1

Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.52, N.54, V.57, E.62 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.52, A:N.54, A:V.57, A:E.62, H2O.8, H2O.8

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

SO4.2: 5 residues within 4Å: Chain A: H.40, Q.174, G.175, S.177 Ligands: TL4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.175, A:S.177 Water bridges: A:H.40, A:S.177, A:S.177 Salt bridges: A:H.40 SO4.3: 2 residues within 4Å: Chain A: K.69, K.89 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.68, A:K.69, A:K.89 Salt bridges: A:K.69, A:K.89

1 x TL4: 2-O-{3-[AMINO(IMINO)METHYL]PHENYL}-5-O-{4-[AMINO(IMINO)METHYL]PHENYL}-1,4:3,6-DIANHYDRO-D-GLUCITOL(Non-covalent)

TL4.4: 16 residues within 4Å: Chain A: E.79, T.80, Y.81, Q.155, D.171, S.172, C.173, S.177, V.191, S.192, W.193, G.194, G.196, C.197, G.204 Ligands: SO4.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.81, A:V.191, A:W.193, A:W.193 Hydrogen bonds: A:T.80, A:Q.155, A:D.171, A:S.172, A:G.194, A:G.196 Water bridges: A:V.205

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 6 residues within 4Å: Chain A: Y.5, C.7, T.11, V.12, L.117, C.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.5, A:Y.5

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: V.58, E.62, Q.63, F.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.64, A:F.64

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: R.49, I.55, N.56, V.57, V.58, F.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.49, A:R.49, A:N.56, A:N.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Fenza, A. et al., Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions. Chemmedchem (2007)

Release Date

2005-12-13

Peptides

Trypsin, cationic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

Trypsin, cationic

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