MolNFT v1 · #23579 · protein
Structure of the ACK1 kinase domain bound to debromohymenialdisine
1U4D · Activated CDC42 kinase 1: “Structure of the ACK1 kinase domain bound to debromohymenialdisine”. X-ray diffraction, 2 ligands (DBQ, CL), 4 pockets (best druggability 0.72). MolNFT v1 #23579 on GenesisL1: 3D structure, binding sites…
- PDB
- 1U4D
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated CDC42 kinase 1
- EC
- 2.7.1.112
- UniProt
- Q07912
- Ligands
- DBQ, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated CDC42 kinase 1 (EC 2.7.1.112) | protein | 258 | 43% helix, 22% strand | Q07912 |
| B | Activated CDC42 kinase 1 (EC 2.7.1.112) | protein | 262 | 39% helix, 21% strand | Q07912 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.72 | 0.79 | 77 | DBQ |
| 2 | 224 | 0.66 | 0.84 | 28 | DBQ |
| 3 | 289 | 0.57 | 0.77 | 37 | empty |
| 4 | 53 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1U4D · Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine · the same entry in another collection · chain A against A, TM-score 1.00
- Q07912 · AlphaFold monomer V2.0 prediction for activated CDC42 kinase 1 (Q07912) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q07912
- Elsewhere: RCSB PDB 1U4D · PDBe 1U4D · UniProt Q07912
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