MolNFT v1 · #114346 · protein
Crystal structure of P21-activated kinase 4 in complex with an inhibitor compound 29
5BMS · SERINE/THREONINE-protein kinase pak 4: “Crystal structure of P21-activated kinase 4 in complex with an inhibitor compound 29”. X-ray diffraction, 1 ligand (4T6), 3 pockets (best druggability 0.61). MolNFT v1 #114346 on GenesisL1: 3D…
- PDB
- 5BMS
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 4
- EC
- 2.7.11.1
- UniProt
- O96013
- Ligands
- 4T6
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 4 (EC 2.7.11.1) | protein | 291 | 40% helix, 19% strand | O96013 |
Ligands and binding sites
- 4T6 · N~2~-[(7-chloro-1H-benzimidazol-6-yl)methyl]-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.61 | 0.79 | 33 | 4T6 |
| 2 | 81 | 0.42 | 0.79 | 17 | empty |
| 3 | 61 | 0.33 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5BMS · Crystal structure of P21-activated kinase 4 in complex with an inhibitor compound 29 · the same entry in another collection · chain A against A, TM-score 1.00
- O96013 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 4 (O96013) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O96013
- Elsewhere: RCSB PDB 5BMS · PDBe 5BMS · UniProt O96013
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