SMTL ID : 1z6j.1

Crystal Structure of a ternary complex of Factor VIIa/Tissue Factor/Pyrazinone Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.46, G.47, Q.49, D.63, Q.64 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.46, A:G.47, A:D.63, A:Q.64 CA.3: 5 residues within 4Å: Chain B: E.58, D.60, E.63, H.64, E.68 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:D.60, B:E.63, B:E.68, H2O.6, H2O.8

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP)

1 x PY3: 5-[AMINO(IMINO)METHYL]-2-[({[6-[3-AMINO-5-({[(1R)-1-METHYLPROPYL]AMINO}CARBONYL)PHENYL]-3-(ISOPROPYLAMINO)-2-OXOPYRAZIN-1(2H)-YL]ACETYL}AMINO)METHYL]-N-PYRIDIN-4-YLBENZAMIDE(Non-covalent)

PY3.4: 23 residues within 4Å: Chain B: H.41, C.42, D.44, K.45, Y.82, P.84, G.85, T.86, 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, G.223, V.224 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:H.41, B:K.45, B:V.210, B:W.212 Hydrogen bonds: B:H.41, B:D.44, B:G.85, B:S.187, B:K.189, B:K.189, B:S.192, B:S.211, B:G.213, B:G.213, B:G.213, B:G.215, B:V.224 Water bridges: B:G.190, B:W.212, B:Q.214, B:G.215 pi-Cation interactions: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schweitzer, B.A. et al., Structure-based design and synthesis of pyrazinones containing novel P1 'side pocket' moieties as inhibitors of TF/VIIa. Bioorg.Med.Chem.Lett. (2005)

Release Date

2005-05-03

Peptides

Coagulation factor VII: A
Coagulation factor VII: B
Tissue factor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
T

Coagulation factor VII

Coagulation factor VII

Tissue factor

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