SMTL ID : 6t7p.1

human plasmakallikrein protease domain in complex with active site directed inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 6 residues within 4Å: Chain A: W.14, P.111, I.112, C.113, M.199, W.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.111, A:C.113, A:W.200 Salt bridges: A:K.110

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

DMS.2: 4 residues within 4Å: Chain A: G.60, T.106, F.108, Q.109 No protein-ligand interaction detected (PLIP) DMS.3: 2 residues within 4Å: Chain A: W.9, F.108 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.9, A:W.9 DMS.4: 6 residues within 4Å: Chain A: D.53, V.54, W.55, R.56, F.73, Q.75 No protein-ligand interaction detected (PLIP) DMS.5: 6 residues within 4Å: Chain A: Q.19, Q.25, R.26, H.27, L.64, I.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.19 DMS.6: 9 residues within 4Å: Chain A: W.9, G.10, W.12, P.13, G.60, I.61, L.62, F.108, L.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.10 Water bridges: A:W.12 DMS.7: 5 residues within 4Å: Chain A: V.20, L.28, L.49, L.51, W.55 No protein-ligand interaction detected (PLIP) DMS.8: 4 residues within 4Å: Chain A: E.140, I.141, Q.142, N.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.143 Water bridges: A:N.143, A:I.144 Salt bridges: A:E.140 DMS.9: 5 residues within 4Å: Chain A: Y.176, E.178, G.179, G.180, K.181 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.176 DMS.10: 5 residues within 4Å: Chain A: A.225, E.226, Y.227, M.228, D.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.228, A:D.229 Water bridges: A:W.230 Salt bridges: A:E.226, A:D.229 DMS.11: 3 residues within 4Å: Chain A: K.195, H.196, N.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.197

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 4 residues within 4Å: Chain A: H.82, Q.83, R.170, W.230 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.83 Water bridges: A:R.170, A:R.170, A:W.230, A:W.230 Salt bridges: A:H.82, A:R.170

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 4 residues within 4Å: Chain A: W.12, W.128, K.147, W.200 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.11, A:K.147, A:K.147, A:W.200

1 x MU8: (2~{S},4~{R})-1-[[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-6-yl]carbonyl]-~{N}-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide(Non-covalent)

MU8.14: 19 residues within 4Å: Chain A: R.26, H.27, L.28, H.44, I.141, D.182, A.183, C.184, K.185, G.186, D.187, S.188, T.206, S.207, W.208, G.209, G.211, C.212, G.219 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.185, A:T.206 Hydrogen bonds: A:G.186, A:D.187, A:S.188, A:G.211 Water bridges: A:L.28, A:L.28, A:S.188, A:S.207 Halogen bonds: A:H.27

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

Plasma kallikrein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Plasma kallikrein