SMTL ID : 4jzd.1

Structure of factor VIIA in complex with the inhibitor 2-{2-[(4-carbamimidoylphenyl)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 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

2 x 1NJ: 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid(Non-covalent)(Non-functional Binders)

1NJ.1: 19 residues within 4Å: Chain A: Q.24, C.26, H.41, T.141, D.186, S.187, K.189, G.190, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 Ligands: 1NJ.2, SO4.6, GOL.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.24, A:H.41, A:K.189, A:V.210 Hydrogen bonds: A:D.186, A:S.187, A:S.187, A:K.189, A:G.190, A:S.192, A:S.192, A:S.211 Water bridges: A:W.212, A:T.218 Salt bridges: A:H.41 pi-Stacking: A:H.41 1NJ.2: 3 residues within 4Å: Ligands: 1NJ.1, SO4.4, SO4.6 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: R.71, R.72, H.97, Q.98 No protein-ligand interaction detected (PLIP)

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

SO4.4: 5 residues within 4Å: Chain A: Q.134, R.138, K.189 Ligands: 1NJ.2, SO4.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.134 Water bridges: A:Q.134, A:R.138, A:R.138, A:R.138 Salt bridges: A:K.189 SO4.5: 3 residues within 4Å: Chain A: M.154, T.155, R.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.155 Water bridges: A:R.152, A:Q.156, A:R.227 Salt bridges: A:R.227 SO4.6: 4 residues within 4Å: Chain A: K.189 Ligands: 1NJ.1, 1NJ.2, SO4.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.189, A:K.189 Salt bridges: A:K.45, A:K.189 SO4.7: 3 residues within 4Å: Chain A: T.86, T.87, P.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.87 Water bridges: A:T.87, A:N.88, A:N.170 SO4.8: 4 residues within 4Å: Chain A: E.68, Q.69, S.70, R.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.70, A:S.70 Water bridges: A:R.71, A:R.71 Salt bridges: A:R.71 SO4.10: 5 residues within 4Å: Chain A: R.119 Chain B: C.2, C.13, S.14, D.15 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.119 Hydrogen bonds: B:C.13, B:D.15, B:D.15

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: L.25, C.26, H.41, C.42 Ligands: 1NJ.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.41

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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