SMTL ID : 3zdu.1

Crystal structure of the human CDKL3 kinase domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 38R: [4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile(Non-covalent)

38R.1: 19 residues within 4Å: Chain A: V.11, G.12, Y.16, V.19, A.32, K.34, F.80, E.81, F.82, I.83, D.84, H.85, T.86, D.89, E.130, N.131, L.133, C.143, D.144 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.19, A:A.32, A:F.80, A:F.80, A:F.80 Hydrogen bonds: A:V.11, A:I.83, A:I.83, A:I.83 38R.7: 19 residues within 4Å: Chain B: V.11, G.12, Y.16, V.19, A.32, K.34, F.80, E.81, F.82, I.83, D.84, H.85, T.86, D.89, E.130, N.131, L.133, C.143, D.144 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.19, B:A.32, B:F.80, B:F.80, B:F.80 Hydrogen bonds: B:V.11, B:I.83, B:I.83, B:I.83

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: D.176, H.224 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.176, A:D.176, A:H.224, H2O.4 ZN.3: 3 residues within 4Å: Chain A: H.93 Chain B: H.212, V.239 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.93, B:H.212, H2O.2, H2O.2, H2O.2 ZN.8: 2 residues within 4Å: Chain B: D.176, H.224 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.176, B:D.176, B:H.224, H2O.10 ZN.9: 3 residues within 4Å: Chain A: H.212, V.239 Chain B: H.93 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.212, B:H.93, H2O.8, H2O.8, H2O.8

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

NA.4: 4 residues within 4Å: Chain A: D.126, D.144, F.147, D.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.159 NA.10: 4 residues within 4Å: Chain B: D.126, D.144, F.147, D.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.126, B:D.159

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

EDO.5: 2 residues within 4Å: Chain A: R.112, M.297 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.112 EDO.6: 4 residues within 4Å: Chain A: R.275, I.276, S.277, D.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.277 EDO.11: 2 residues within 4Å: Chain B: R.112, M.297 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.112 EDO.12: 4 residues within 4Å: Chain B: R.275, I.276, S.277, D.280 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.277, B:D.280

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

2013-03-20

Peptides

CYCLIN-DEPENDENT KINASE-LIKE 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYCLIN-DEPENDENT KINASE-LIKE 3