SMTL ID : 8s6i.1

Crystal structure of the human CDKL2 kinase domain with Compound 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x 01: ~{N}-[6-[3-[(2-methylpropylsulfonylamino)methyl]phenyl]-1~{H}-indazol-3-yl]cyclopropanecarboxamide

01.1: 22 residues within 4Å: Chain A: V.33, G.34, Y.38, V.41, A.54, K.56, L.81, L.86, V.87, F.103, E.104, F.105, V.106, D.107, T.109, L.156, L.165, C.166, D.167, F.168, F.170 Ligands: EDO.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.38, A:V.41, A:L.81, A:L.86, A:T.109, A:L.156, A:F.170 Hydrogen bonds: A:E.104, A:V.106, A:V.106, A:D.167, A:F.168 pi-Stacking: A:Y.38

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

EDO.2: 5 residues within 4Å: Chain A: F.58, L.59, I.70, E.74, T.173 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.173, A:T.173 EDO.3: 4 residues within 4Å: Chain A: K.56, L.101, F.103 Ligands: 01.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.56 Water bridges: A:D.167 EDO.4: 3 residues within 4Å: Chain A: D.232, H.236, M.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.232

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

CL.5: 4 residues within 4Å: Chain A: R.269, P.271, L.272, K.288 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bashore, F.M. et al., Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. Acs Med.Chem.Lett. (2024)

Release Date

2025-02-26

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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