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

Analyse Crystal structure of the human CDKL5 kinase domain with compound YL-354 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8CIE
Type: protein
Length: 280 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Homo sapiens
Molecule: Cyclin-dependent kinase-like 5
EC: 2.7.11.22
UniProt: O76039
Ligands: US0, SO4
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · resolution 2.2 · 1 distinct chain · 40% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase-like 5 (EC 2.7.11.22)	protein	280	40% helix, 14% strand	O76039

Ligands and binding sites

US0 · 4-[[3,5-bis(fluoranyl)phenyl]carbonylamino]-~{N}-piperidin-4-yl-1~{H}-pyrazole-3-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.73	0.90	23	US0
2	54	0.36	0.79	10	empty
3	56	0.30	0.75	14	empty

Compared structures

O76039 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase-like 5 (O76039) · a predicted model of the same protein · chain A against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O76039
Elsewhere: RCSB PDB 8CIE · PDBe 8CIE · UniProt O76039

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