SMTL ID : 9r8r.1

Factor Xa bound to BAY 3389934

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.56, N.58, Q.61, E.63, E.66 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.56, A:N.58, A:Q.61, A:E.63, H2O.1

1 x 01: 2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate

01.2: 21 residues within 4Å: Chain A: H.42, Q.46, E.83, T.84, Y.85, F.162, D.179, A.180, C.181, Q.182, G.183, S.185, V.203, W.205, G.206, E.207, G.208, C.209, G.216, I.217, Y.218 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.85, A:Y.85, A:F.162, A:W.205 Hydrogen bonds: A:G.206, A:G.208, A:G.208, A:G.208

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.192, F.193, K.194, D.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.192, A:K.194, A:D.195, A:D.195 GOL.5: 5 residues within 4Å: Chain A: M.120, V.151, R.153, F.169, K.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.120, A:V.151, A:R.153, A:K.220 Water bridges: A:C.170

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.4: 5 residues within 4Å: Chain A: V.74, K.76, H.77, N.78, W.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.78, A:N.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beck, H. et al., Discovery of BAY 3389934 Hydrochloride: A Potent and Selective Small-Molecule Dual Factor IIa/Xa Inhibitor with Short Half-Life for the Acute Treatment of Sepsis-Induced Coagulopathy. J.Med.Chem. (2025)

Release Date

2025-06-18

Peptides

Coagulation factor X: A
Coagulation factor X: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coagulation factor X

Coagulation factor X

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