SMTL ID : 7neu.1

Inhibitor Complex with Thrombin Activatable Fibrinolysis Inhibitor (TAFIa)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x U9K: (1R,3S)-3-(4-ammoniobutyl)-1-(4-fluoro-2-(1-methyl-1H-imidazol-5-yl)benzyl)-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide(Non-covalent)

U9K.1: 25 residues within 4Å: Chain A: P.33, V.34, L.38, H.158, E.161, R.216, N.233, R.234, H.287, S.288, Y.289, S.290, V.294, S.298, G.335, S.336, T.338, Y.340, L.341, A.342, G.345, D.347, T.360, E.362 Ligands: ZN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.294, A:A.342 Hydrogen bonds: A:H.158, A:R.216, A:N.233, A:H.287, A:T.360, A:T.360 Salt bridges: A:H.158, A:R.216, A:R.234, A:E.362 Halogen bonds: A:S.298

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.158, E.161, R.216, H.287 Ligands: U9K.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.158, A:E.161, A:E.161, A:H.287

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: W.170, H.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.174

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

CL.4: 4 residues within 4Å: Chain A: G.180, I.181, G.183, T.186 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: R.364, D.365, T.368, Y.369, L.373, Y.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.364 Water bridges: A:T.368

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 4 residues within 4Å: Chain A: R.14, Q.17, V.18, N.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.18 Hydrogen bonds: A:Q.17, A:N.21 NAG.7: 5 residues within 4Å: Chain A: S.2, E.27, N.50, A.51, S.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.51, A:S.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schaffner, A.P. et al., Phosphinanes and Azaphosphinanes as Potent and Selective Inhibitors of Activated Thrombin-Activatable Fibrinolysis Inhibitor (TAFIa). J.Med.Chem. (2021)

Release Date

2021-04-07

Peptides

Carboxypeptidase B2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carboxypeptidase B2