SMTL ID : 3kl6.1

Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and orally active factor Xa inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 443: 1-(1-{(2S)-3-[(6-chloronaphthalen-2-yl)sulfonyl]-2-hydroxypropanoyl}piperidin-4-yl)tetrahydropyrimidin-2(1H)-one(Non-covalent)

443.1: 21 residues within 4Å: Chain A: K.82, E.83, T.84, Y.85, F.162, D.179, A.180, C.181, Q.182, S.185, V.203, S.204, W.205, G.206, E.207, G.208, C.209, G.216, I.217, Y.218 Ligands: EDO.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.162, A:F.162, A:A.180, A:V.203, A:W.205 Hydrogen bonds: A:E.83, A:G.206, A:G.208

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

EDO.2: 8 residues within 4Å: Chain A: S.159, S.160, W.205, G.206, E.207, K.214, Y.215, I.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.159, A:S.159, A:E.207 Water bridges: A:G.208, A:Y.215 EDO.3: 4 residues within 4Å: Chain A: R.49, F.50, V.71, V.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.50, A:F.50 EDO.4: 3 residues within 4Å: Chain A: G.208, R.211 Ligands: 443.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.208 EDO.8: 1 residues within 4Å: Chain B: E.21 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: E.111, D.113 Chain B: H.19 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.111, A:E.111, A:D.113, A:D.113, B:H.19 CA.6: 4 residues within 4Å: Chain A: Y.173, D.174, R.211, K.214 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.173, A:D.174, A:R.211, A:K.214, H2O.6 CA.7: 5 residues within 4Å: Chain A: D.56, N.58, Q.61, E.63, E.66 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.56, A:N.58, A:Q.61, A:E.63, A:E.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujimoto, T. et al., Discovery of a tetrahydropyrimidin-2(1H)-one derivative (TAK-442) as a potent, selective, and orally active factor Xa inhibitor. J.Med.Chem. (2010)

Release Date

2009-12-01

Peptides

Coagulation Factor X heavy chain: A
Coagulation Factor X light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coagulation Factor X heavy chain

Coagulation Factor X light chain

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