MolNFT v1 · #84219 · protein
Crystal structure of the human CDKL3 kinase domain
3ZDU · Cyclin-dependent kinase-like 3: “Crystal structure of the human CDKL3 kinase domain”. X-ray diffraction, 3 ligands (38R, ZN, NA), 2 pockets (best druggability 0.73). MolNFT v1 #84219 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ZDU
- Type
- protein
- Length
- 297 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase-like 3
- EC
- 2.7.11.22
- UniProt
- Q8IVW4
- Ligands
- 38R, ZN, NA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase-like 3 (EC 2.7.11.22) | protein | 297 | 45% helix, 15% strand | Q8IVW4 |
Ligands and binding sites
- 38R · [4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.73 | 0.86 | 40 | 38R, NA |
| 2 | 108 | 0.54 | 0.83 | 21 | empty |
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 Q8IVW4
- Elsewhere: RCSB PDB 3ZDU · PDBe 3ZDU · UniProt Q8IVW4
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