SMTL ID : 5u6j.1

Factor VIIa in complex with the inhibitor 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 82J: 3-{[(2R)-17-ethyl-4-methyl-3,12-dioxo-7-[(propan-2-yl)sulfonyl]-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-2-yl]amino}benzamide(Non-covalent)

82J.1: 23 residues within 4Å: Chain A: L.25, C.26, H.41, C.42, D.44, K.45, G.85, T.86, T.87, D.90, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.25, A:T.87, A:V.210, A:W.212 Hydrogen bonds: A:S.192, A:S.192, A:G.215, A:G.215 Water bridges: A:D.44, A:G.85, A:Q.214 pi-Stacking: A:H.41, 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.2, H2O.4

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.72, A:H.97, A:Q.98 Salt bridges: 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.47, A:N.48, 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.162, 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 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:H.26 Hydrogen bonds: A:I.31, A:N.32, A:Q.236 Water bridges: A:L.111

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: F.43, D.44, I.46, W.49, P.84, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.46 GOL.8: 6 residues within 4Å: Chain A: E.11, C.12, L.128, W.204 Chain B: I.49, L.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.11, A:E.11 Water bridges: A:K.5, A:K.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wurtz, N.R. et al., Neutral macrocyclic factor VIIa inhibitors. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-05-10

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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