MolNFT v1 · #101748 · protein
Back pocket flexibility provides group-II pak selectivity for type 1 kinase inhibitors
4O0R · SERINE/THREONINE-protein kinase pak 1: “Back pocket flexibility provides group-II pak selectivity for type 1 kinase inhibitors”. X-ray diffraction, 1 ligand (7KC), 5 pockets (best druggability 0.77). MolNFT v1 #101748 on GenesisL1…
- PDB
- 4O0R
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 1
- EC
- 2.7.11.1
- UniProt
- Q13153
- Ligands
- 7KC
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 293 | 41% helix, 17% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 282 | 42% helix, 15% strand | Q13153 |
Ligands and binding sites
- 7KC · ~{N}-[(1~{S})-2-(dimethylamino)-1-phenyl-ethyl]-6,6-dimethyl-3-[(2-methylthieno[3,2-d]pyrimidin-4-yl) amino]-1,4-dihydropyrrolo[3,4-c]pyrazole-5-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.77 | 0.79 | 94 | 7KC |
| 2 | 241 | 0.58 | 0.79 | 37 | empty |
| 3 | 94 | 0.54 | 0.84 | 19 | empty |
| 4 | 63 | 0.37 | 0.78 | 14 | empty |
| 5 | 53 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 843 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4O0R · Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- Q13153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 1 (Q13153) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13153
- Elsewhere: RCSB PDB 4O0R · PDBe 4O0R · UniProt Q13153
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