SMTL ID : 8cie.1

Crystal structure of the human CDKL5 kinase domain with compound YL-354

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x US0: 4-[[3,5-bis(fluoranyl)phenyl]carbonylamino]-~{N}-piperidin-4-yl-1~{H}-pyrazole-3-carboxamide(Non-covalent)

US0.1: 18 residues within 4Å: Chain A: V.20, Y.25, V.28, A.41, K.43, F.90, E.91, Y.92, V.93, E.94, K.95, N.96, E.99, E.140, N.141, L.143, C.153, D.154 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.20, A:Y.25, A:V.28, A:Y.92, A:D.154 Hydrogen bonds: A:E.91, A:V.93, A:V.93, A:E.99 Halogen bonds: A:E.140

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: Y.92, V.93, E.94, S.145, H.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.94, A:H.146 Salt bridges: A:H.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ong, H.W. et al., Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective. Acs Chem Neurosci (2023)

Release Date

2023-06-14

Peptides

Cyclin-dependent kinase-like 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclin-dependent kinase-like 5

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