SMTL ID : 2c4f.1

crystal structure of factor VII.stf complexed with pd0297121

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.58, D.60, E.63, H.64, 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.5 CA.3: 5 residues within 4Å: Chain B: D.46, G.47, Q.49, D.63, Q.64 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.46, B:G.47, B:D.63, B:Q.64, H2O.8 CA.6: 2 residues within 4Å: Chain B: E.16, E.26 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain B: E.14, E.19 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain B: E.25, R.28, E.29 No protein-ligand interaction detected (PLIP)

1 x GIL: 2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BEN ZOIC ACID(Non-covalent)

GIL.2: 19 residues within 4Å: Chain A: Q.24, H.41, G.85, T.86, T.87, Q.134, T.141, D.186, S.187, C.188, K.189, G.190, S.192, V.210, S.211, W.212, G.213, C.216, G.223 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.141, A:K.189, A:K.189, A:V.210, A:W.212, A:W.212 Hydrogen bonds: A:D.186, A:S.187, A:G.190, A:S.192 Water bridges: A:V.224 Salt bridges: A:H.41 pi-Cation interactions: A:H.41 Halogen bonds: A:G.213

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.4: 4 residues within 4Å: Chain B: Q.49, S.52, P.54, Y.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.49, B:S.52

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.5: 7 residues within 4Å: Chain B: G.58, G.59, S.60, F.71, L.73 Chain D: R.41, F.50 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.73, D:F.50 Salt bridges: D:R.41

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 5 residues within 4Å: Chain D: E.27, N.34, T.36, E.80, L.82 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:N.34, D:L.82 Hydrogen bonds: D:E.27, D:T.36 Water bridges: D:N.34, D:E.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kohrt, J.T. et al., The Discovery of Fluoropyridine-Based Inhibitors of the Factor Viia/Tf Complex--Part 2. Bioorg.Med.Chem.Lett. (2006)

Release Date

2006-10-18

Peptides

COAGULATION FACTOR VII PRECURSOR: A
COAGULATION FACTOR VII PRECURSOR: B
TISSUE FACTOR PRECURSOR: C
TISSUE FACTOR PRECURSOR: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
T

D
U

COAGULATION FACTOR VII PRECURSOR

COAGULATION FACTOR VII PRECURSOR

TISSUE FACTOR PRECURSOR

TISSUE FACTOR PRECURSOR

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