MolNFT v1 · #86778 · protein
Crystal structure of the human CDKL5 kinase domain
4BGQ · Cyclin-dependent kinase-like 5: “Crystal structure of the human CDKL5 kinase domain”. X-ray diffraction, 2 ligands (38R, NA), 1 pocket (best druggability 0.73). MolNFT v1 #86778 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4BGQ
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase-like 5
- EC
- 2.7.11.22
- UniProt
- O76039
- Ligands
- 38R, NA
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase-like 5 (EC 2.7.11.22) | protein | 276 | 41% helix, 18% strand | O76039 |
Ligands and binding sites
- 38R · [4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile · ligand · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.73 | 0.86 | 36 | 38R |
Compared structures
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 4BGQ · PDBe 4BGQ · UniProt O76039
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