MolNFT v1 · #90691 · protein
Human stk-10 (lok) kinase domain in dfg-out conformation with inhibitor dsa-7
4EQU · SERINE/THREONINE-protein kinase 10: “Human stk-10 (lok) kinase domain in dfg-out conformation with inhibitor dsa-7”. X-ray diffraction, 2 ligands (G6I, CA), 5 pockets (best druggability 0.71). MolNFT v1 #90691 on GenesisL1: 3D…
- PDB
- 4EQU
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 10
- EC
- 2.7.11.1
- UniProt
- O94804
- Ligands
- G6I, CA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 10 (EC 2.7.11.1) | protein | 274 | 42% helix, 16% strand | O94804 |
| B | SERINE/THREONINE-protein kinase 10 (EC 2.7.11.1) | protein | 282 | 41% helix, 17% strand | O94804 |
Ligands and binding sites
- G6I · N-{3-[(3-{4-[(4-methoxyphenyl)amino]-1,3,5-triazin-2-yl}pyridin-2-yl)amino]-4-methylphenyl}-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A, B
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 | 318 | 0.71 | 0.84 | 45 | G6I |
| 2 | 257 | 0.70 | 0.85 | 33 | G6I |
| 3 | 352 | 0.57 | 0.75 | 42 | 1PE |
| 4 | 101 | 0.48 | 0.81 | 16 | empty |
| 5 | 96 | 0.47 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1793 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4EQU · Human STK-10 (LOK) kinase domain in DFG-out conformation with inhibitor DSA-7 · the same entry in another collection · chain A against A, TM-score 1.00
- O94804 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase 10 (O94804) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 O94804
- Elsewhere: RCSB PDB 4EQU · PDBe 4EQU · UniProt O94804
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