SMTL ID : 4jzf.1

Structure of factor VIIA in complex with the inhibitor 2-{2-[(3-carbamoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 1NL: 2-{2-[(3-carbamoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid(Non-covalent)

1NL.1: 18 residues within 4Å: Chain A: Q.24, L.25, H.41, T.87, T.141, D.186, S.187, C.188, K.189, G.190, S.192, V.210, S.211, W.212, G.213, G.215, C.216 Ligands: GOL.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.24, A:K.189, A:V.210 Hydrogen bonds: A:G.190, A:S.192, A:S.192, A:S.211, A:G.215, A:G.215 Water bridges: A:Q.214 Salt bridges: A:H.41 pi-Stacking: A:H.41

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.58, D.60, E.63, E.68 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.58, A:D.60, A:E.63, A:E.68, H2O.3, H2O.10

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

SO4.3: 4 residues within 4Å: Chain A: R.71, R.72, H.97, Q.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.72, A:H.97, 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.21, A:K.45, A:K.47, A:N.48 SO4.5: 7 residues within 4Å: Chain A: C.158, 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:Q.214, A:F.222 Salt bridges: A:H.221 SO4.6: 5 residues within 4Å: Chain A: I.31, N.32, Q.236, M.239 Chain B: H.26 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:E.27, B:E.27 Salt bridges: B:H.26 Hydrogen bonds: A:I.31, A:N.32, A:Q.236, A:Q.236

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: L.25, C.26, H.41, C.42 Ligands: 1NL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.41 GOL.8: 4 residues within 4Å: Chain A: F.43, D.44, W.49, P.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.43 GOL.9: 5 residues within 4Å: Chain A: E.11, C.12, L.128, W.204 Chain B: I.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.11, A:E.11 Water bridges: A:K.5, A:W.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bolton, S.A. et al., Discovery of nonbenzamidine factor VIIa inhibitors using a biaryl acid scaffold. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-08-21

Peptides

Factor VIIa (Heavy Chain): A
Factor VIIa (Light Chain): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Factor VIIa (Heavy Chain)

Factor VIIa (Light Chain)

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