SMTL ID : 4txc.1

Crystal Structure of DAPK1 kinase domain in complex with a small molecule inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x 38G: 4-(3-{3-[(R)-{[2-(dimethylamino)ethyl]amino}(hydroxy)methyl]phenyl}imidazo[1,2-b]pyridazin-6-yl)-2-methoxyphenol(Non-covalent)

38G.1: 16 residues within 4Å: Chain A: L.38, G.39, V.46, A.59, K.61, E.83, I.96, L.112, E.113, V.115, E.162, N.163, M.165, I.179, D.180, F.181 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.38, A:A.59, A:I.96, A:I.96, A:L.112, A:I.179 Hydrogen bonds: A:V.115, A:D.180, A:F.181 Water bridges: A:S.40, A:K.61 Salt bridges: A:E.162, A:D.180

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: V.45, F.62, K.64, D.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.107 EDO.3: 5 residues within 4Å: Chain A: P.212, L.213, G.214, E.216, P.279 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.206, A:P.212, A:L.213, A:G.214 EDO.4: 1 residues within 4Å: Chain A: E.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.192 EDO.5: 3 residues within 4Å: Chain A: Y.253, F.255, R.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:R.272, A:R.272 EDO.6: 6 residues within 4Å: Chain A: F.121, L.124, I.228, L.229, G.232 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: L.229, L.230, S.231, G.232 Ligands: EDO.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilbek, T.S. et al., Identification and characterization of a small-molecule inhibitor of death-associated protein kinase 1. Chembiochem (2015)

Release Date

2014-07-23

Peptides

Death-associated protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Death-associated protein kinase 1