MolNFT v1 · #157082 · protein
Crystal structure of mouse btk kinase domain in complex with compound 9A
6MNY · Tyrosine-protein kinase: “Crystal structure of mouse btk kinase domain in complex with compound 9A”. X-ray diffraction, 1 ligand (JVP), 4 pockets (best druggability 0.82). MolNFT v1 #157082 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MNY
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase
- EC
- 2.7.10.2
- UniProt
- Q7TMU1
- Ligands
- JVP
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 252 | 43% helix, 19% strand | Q7TMU1 |
| B | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 253 | 43% helix, 18% strand | Q7TMU1 |
Ligands and binding sites
- JVP · 5-amino-1-[(3R)-1-cyanopiperidin-3-yl]-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazole-4-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.82 | 0.83 | 88 | empty |
| 2 | 279 | 0.70 | 0.85 | 41 | JVP |
| 3 | 54 | 0.43 | 0.83 | 16 | empty |
| 4 | 78 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MNY · Crystal structure of mouse BTK kinase domain in complex with compound 9a · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7TMU1
- Elsewhere: RCSB PDB 6MNY · PDBe 6MNY · UniProt Q7TMU1
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