SMTL ID : 4yt6.1

Factor VIIa in complex with the inhibitor 4-{[(R)-[5-ethoxy-2-fluoro-3-(propan-2-yloxy)phenyl](4-phenyl-1H-imidazol-2-yl)methyl]amino}benzenecarboximidamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 4JY: 4-[[(R)-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)-(4-phenyl-1H-imidazol-2-yl)methyl]amino]benzenecarboximidamide(Non-covalent)

4JY.1: 23 residues within 4Å: Chain A: L.25, C.26, H.41, C.42, K.45, T.86, T.87, D.90, P.169, D.186, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, Q.214, G.215, C.216, A.217, G.223 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.25, A:H.41, A:V.210 Hydrogen bonds: A:D.186, A:S.192, A:S.192, A:G.215 Water bridges: A:W.212

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.58, D.60, E.63, E.68 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.58, A:D.60, A:E.68, H2O.3, H2O.6

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

SO4.3: 5 residues within 4Å: Chain A: S.70, R.71, R.72, H.97, Q.98 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.72, A:H.97, A:Q.98, A:Q.98 Salt bridges: A:R.72, A:H.97 SO4.4: 6 residues within 4Å: Chain A: V.20, N.21, K.45, I.46, K.47, N.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.21, A:K.47, A:N.48 SO4.5: 6 residues within 4Å: Chain A: S.162, I.171, Q.214, H.221, F.222, V.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.162, A:F.222, A:F.222 Salt bridges: A:H.221 SO4.6: 7 residues within 4Å: Chain A: I.31, N.32, L.111, Q.236, M.239 Chain B: H.28 Ligands: GOL.9 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.32, A:Q.236 Water bridges: B:H.28, B:E.29 Salt bridges: B:H.28

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: F.43, D.44, W.49, I.78, P.84, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.43 GOL.8: 8 residues within 4Å: Chain A: C.7, E.11, C.12, L.128, V.147, W.204 Chain B: I.51, L.54 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.14, A:W.204 GOL.9: 4 residues within 4Å: Chain A: Q.236, M.239, R.240 Ligands: SO4.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glunz, P.W. et al., Design and synthesis of potent, selective phenylimidazole-based FVIIa inhibitors. Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-04-29

Peptides

Coagulation factor VII (heavy chain): A
Coagulation factor VII (light chain): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Coagulation factor VII (heavy chain)

Coagulation factor VII (light chain)

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