SMTL ID : 4yzu.1

Rapid development of two Factor IXa inhibitors from Hit to Lead

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 4K6: N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide(Non-covalent)

4K6.1: 13 residues within 4Å: Chain A: Y.86, F.162, S.180, C.181, Q.182, D.184, S.185, I.203, W.205, G.206, E.207, C.209, G.216 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.86, A:F.162, A:I.203, A:W.205 Hydrogen bonds: A:E.207 Water bridges: A:N.84, A:N.84, A:Q.182 pi-Stacking: A:F.162, A:W.205

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 8 residues within 4Å: Chain A: E.55, H.56, N.57, I.58, E.60, T.61, E.62, E.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.57, A:E.62, A:E.65 Water bridges: A:E.55

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.3: 7 residues within 4Å: Chain A: D.6, V.133, F.134, A.140, L.141, V.142, Q.144 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:L.141, A:V.142 Water bridges: A:D.6

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain B: R.33, L.34 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parker, D.L. et al., Rapid development of two factor IXa inhibitors from hit to lead. Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-05-20

Peptides

Coagulation factor IX: A
Coagulation factor IX: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coagulation factor IX

Coagulation factor IX

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