SMTL ID : 6x5j.1

Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: N.84, Y.86, N.87, F.162, T.163, I.164, Y.165, M.168, W.205 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.84, A:N.84, A:Y.86, A:T.163 Water bridges: A:T.163 GOL.2: 7 residues within 4Å: Chain A: N.78, Y.79, N.80, I.83, N.84, N.87, H.88 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.78, A:N.84, A:N.87, A:H.88 Water bridges: A:N.78, A:N.87

1 x 6NH: 2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE(Non-covalent)

6NH.3: 23 residues within 4Å: Chain A: F.25, C.26, H.41, C.42, K.85, Y.86, D.179, S.180, C.181, Q.182, G.183, D.184, S.185, I.203, S.204, W.205, G.206, E.207, E.208, C.209, A.210, G.216 Ligands: CIT.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.25 Hydrogen bonds: A:H.41, A:S.180, A:S.180, A:S.185, A:E.207 Water bridges: A:S.185, A:W.205 pi-Stacking: A:H.41

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

NA.4: 8 residues within 4Å: Chain A: E.55, H.56, N.57, I.58, E.60, T.61, E.62, E.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.62, A:E.65

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 7 residues within 4Å: Chain A: N.87, H.88, Y.165, N.166, N.167, R.223 Ligands: CIT.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.165 Hydrogen bonds: A:N.166, A:N.166, A:N.167, A:N.167 Salt bridges: A:H.88, A:R.223 CIT.6: 4 residues within 4Å: Chain A: N.166, N.167, R.223 Ligands: CIT.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.166, A:N.167 Water bridges: A:K.113, A:K.113 Salt bridges: A:K.113 CIT.7: 8 residues within 4Å: Chain A: H.76, H.77, N.78, R.223, Y.224, V.225, N.226, W.227 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.227 Hydrogen bonds: A:H.76, A:R.223, A:N.226, A:N.226, A:W.227 Water bridges: A:H.77, A:R.223, A:V.225, A:V.225 Salt bridges: A:H.76, A:H.76, A:H.77, A:H.77, A:R.223 CIT.8: 7 residues within 4Å: Chain A: Y.86, Q.182, W.205, G.206, E.207, C.209 Ligands: 6NH.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.86, A:G.206, A:G.206, A:E.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jayne, C.L. et al., Discovery of hydroxy pyrimidine Factor IXa inhibitors. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-06-24

Peptides

Coagulation factor IX: A
Coagulation factor IX: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coagulation factor IX

Coagulation factor IX

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