MolNFT v1 · #86031 · protein
Crystal structure of compound 4A in complex with CDK5, showing an unusual binding mode to the hinge region via a water molecule
4AU8 · Cyclin-dependent kinase 5: “Crystal structure of compound 4A in complex with CDK5, showing an unusual binding mode to the hinge region…”. X-ray diffraction, 2 ligands (Z3R, SO4), 9 pockets (best druggability 0.67). MolNFT v1 #86031…
- PDB
- 4AU8
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 5
- EC
- 2.7.11.22
- UniProt
- Q00535
- Ligands
- Z3R, SO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 5 (EC 2.7.11.22) | protein | 276 | 39% helix, 17% strand | Q00535 |
| B | Cyclin-dependent kinase 5 (EC 2.7.11.22) | protein | 277 | 38% helix, 18% strand | Q00535 |
Ligands and binding sites
- Z3R · 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.67 | 0.89 | 22 | Z3R |
| 2 | 130 | 0.65 | 0.87 | 22 | Z3R |
| 3 | 80 | 0.47 | 0.82 | 18 | empty |
| 4 | 147 | 0.46 | 0.77 | 16 | empty |
| 5 | 80 | 0.46 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4AU8 · Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to… · the same entry in another collection · chain B against B, TM-score 1.00
- Q00535 · AlphaFold monomer V2.0 prediction for cyclin-dependent-like kinase 5 (Q00535) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q00535
- Elsewhere: RCSB PDB 4AU8 · PDBe 4AU8 · UniProt Q00535
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