Research workbench
Structure of P21-activated kinase 4 with a novel inhibitor ky-04031
Analyse Structure of P21-activated kinase 4 with a novel inhibitor ky-04031 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NJD
- 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
- NJD
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 38% 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 | 38% helix, 19% strand | O96013 |
Ligands and binding sites
- NJD · N-(1H-indazol-5-yl)-N'-[2-(1H-indol-3-yl)ethyl]-6-methoxy-1,3,5-triazine-2,4-diamine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.67 | 0.81 | 46 | NJD |
| 2 | 51 | 0.32 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4NJD · Structure of p21-activated kinase 4 with a novel inhibitor KY-04031 · 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 0.98
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 O96013
- Elsewhere: RCSB PDB 4NJD · PDBe 4NJD · UniProt O96013
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