SMTL ID : 6ts4.1

Coagulation factor XI protease domain in complex with active site inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

monomer

Ligands

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

SO4.1: 1 residues within 4Å: Ligands: DMS.8 No protein-ligand interaction detected (PLIP) SO4.2: 4 residues within 4Å: Chain A: K.117, G.118, D.119, R.120 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.118, A:D.119, A:R.120 Water bridges: A:R.120, A:R.120, A:R.120, A:R.120, A:R.120 Salt bridges: A:R.120 SO4.3: 3 residues within 4Å: Chain A: Q.84, Y.92, K.170 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.84 Water bridges: A:Y.92, A:Y.92, A:K.170, A:K.170 Salt bridges: A:K.170

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

DMS.4: 4 residues within 4Å: Chain A: T.154, N.155, E.156, H.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.155, A:E.156 DMS.5: 5 residues within 4Å: Chain A: Y.124, L.152, I.172, V.203, N.223 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.124, A:Y.124 DMS.6: 3 residues within 4Å: Chain A: F.73, F.74, T.101 No protein-ligand interaction detected (PLIP) DMS.7: 2 residues within 4Å: Chain A: H.196, N.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.197 Water bridges: A:E.198 DMS.8: 6 residues within 4Å: Chain A: G.10, E.11, W.14, R.110, W.200 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.110, A:R.110

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

NA.9: 4 residues within 4Å: Chain A: E.226, Y.227, D.229, W.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.226, A:D.229, A:W.230

1 x J7B: 2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid(Non-covalent)

J7B.10: 16 residues within 4Å: Chain A: L.28, C.29, H.44, C.45, D.182, A.183, C.184, K.185, G.186, D.187, A.188, T.206, W.208, G.209, G.211, C.212 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.183, A:K.185, A:K.185, A:T.206 Hydrogen bonds: A:G.186, A:A.188, A:G.211 Water bridges: A:A.183 Salt bridges: A:H.44 pi-Stacking: A:H.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorthiois, E. et al., Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach. J.Med.Chem. (2020)

Release Date

2020-07-08

Peptides

Coagulation factor XI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Coagulation factor XI