SMTL ID : 4aaa.1

Crystal structure of the human CDKL2 kinase domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x DKI: 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE(Non-covalent)

DKI.1: 20 residues within 4Å: Chain A: V.33, G.34, Y.38, V.41, A.54, V.87, F.103, E.104, F.105, V.106, D.107, H.108, T.109, D.112, E.153, N.154, L.156, C.166, D.167 Ligands: EDO.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.33, A:Y.38, A:Y.38, A:F.105, A:T.109, A:D.167 Hydrogen bonds: A:E.104, A:V.106, A:V.106, A:D.112 Water bridges: A:G.34, A:Y.38, A:Y.38 Halogen bonds: A:E.153

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

EDO.2: 5 residues within 4Å: Chain A: V.87, F.103, C.166, D.167 Ligands: DKI.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.167, A:D.167, A:D.167 Water bridges: A:F.168 EDO.3: 2 residues within 4Å: Chain A: D.112, E.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.112, A:E.115 EDO.4: 4 residues within 4Å: Chain A: I.266, K.267, E.268, R.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.267, A:R.269 Water bridges: A:R.269 EDO.5: 5 residues within 4Å: Chain A: N.243, L.244, I.245, P.246, I.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.243 EDO.6: 4 residues within 4Å: Chain A: M.24, Y.27, N.29, C.44 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: G.50, R.51, I.52 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Canning, P. et al., CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function. Cell Rep (2018)

Release Date

2011-12-21

Peptides

CYCLIN-DEPENDENT KINASE-LIKE 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CYCLIN-DEPENDENT KINASE-LIKE 2

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