SMTL ID : 6t9u.1

Bovine Trypsine in complex with the synthetic inhibitor (S)-3'-(N-(1-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-3-(3-carbamimidoylphenyl)-1-oxopropan-2-yl)sulfamoyl)-[1,1'-biphenyl]-3-carboximidamide (MI-490)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

monomer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 7 residues within 4Å: Chain A: Y.28, C.30, T.34, V.35, L.140, C.160, K.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.28 DMS.3: 7 residues within 4Å: Chain A: P.129, T.130, S.131, C.132, A.133, K.209, Q.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.130, A:S.131, A:Q.211

1 x MZE: 1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-(3-carbamimidoylphenyl)phenyl]sulfonylamino]propanoyl]piperidin-4-yl]urea(Non-covalent)

MZE.2: 21 residues within 4Å: Chain A: H.63, N.102, T.103, L.104, Q.178, D.194, S.195, C.196, Q.197, S.200, V.214, S.215, W.216, G.217, S.218, G.219, C.220, A.221, G.227, V.228 Ligands: TFA.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.104, A:V.214, A:W.216 Hydrogen bonds: A:Q.178, A:D.194, A:S.195, A:G.217, A:G.219, A:G.219, A:G.219 Water bridges: A:Q.178, A:V.228 pi-Stacking: A:W.216

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.4: 6 residues within 4Å: Chain A: F.47, H.63, Q.197, G.198, S.200 Ligands: MZE.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.198, A:S.200, A:S.200 Salt bridges: A:H.63

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 8 residues within 4Å: Chain A: E.75, D.76, N.77, I.78, V.80, V.81, E.82, E.85 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.75, A:N.77, A:V.80, A:E.85, H2O.1, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pilgram, O. et al., Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors. Eur.J.Med.Chem. (2022)

Release Date

2020-11-18

Peptides

Cationic Trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cationic Trypsin

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