MolNFT v1 · #167628 · protein
Crystal structure analysis of human ACK1
6VQM · Activated CDC42 kinase 1: “Crystal structure analysis of human ACK1”. X-ray diffraction, 2 ligands (R7P, SO4), 4 pockets (best druggability 0.67). MolNFT v1 #167628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VQM
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated CDC42 kinase 1
- EC
- 2.7.10.2, 2.7.11.1
- UniProt
- Q07912
- Ligands
- R7P, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated CDC42 kinase 1 (EC 2.7.10.2, 2.7.11.1) | protein | 267 | 38% helix, 21% strand | Q07912 |
| B | Activated CDC42 kinase 1 (EC 2.7.10.2, 2.7.11.1) | protein | 267 | 37% helix, 20% strand | Q07912 |
Ligands and binding sites
- R7P · 2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]-2-methoxyphenyl}amino)-9-methyl-5,7-dihydro-6H-pyrimido[5,4-d][1,3]benzodiazepin-6-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
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 | 427 | 0.67 | 0.79 | 50 | R7P |
| 2 | 275 | 0.61 | 0.80 | 34 | R7P |
| 3 | 352 | 0.61 | 0.77 | 51 | empty |
| 4 | 153 | 0.42 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 5 hydrogen bonds · protein-protein
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 Q07912
- Elsewhere: RCSB PDB 6VQM · PDBe 6VQM · UniProt Q07912
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