MolNFT v1 · #135785 · protein
Discovery of a potent btk inhibitor with a novel binding mode using parallel selections with a DNA-encoded chemical library
5U9D · Tyrosine-protein kinase btk: “Discovery of a potent btk inhibitor with a novel binding mode using parallel selections with a DNA-encoded…”. X-ray diffraction, 1 ligand (83P), 4 pockets (best druggability 0.72). MolNFT v1 #135785 on…
- PDB
- 5U9D
- Type
- protein
- Length
- 271 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase btk
- EC
- 2.7.10.2
- UniProt
- Q06187
- Ligands
- 83P
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 271 | 42% helix, 17% strand | Q06187 |
Ligands and binding sites
- 83P · (R)-N-methyl-2-(3-((quinoxalin-6-ylamino)methyl)furan-2-carbonyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.98 | 16 | empty |
| 2 | 351 | 0.62 | 0.78 | 46 | 83P |
| 3 | 92 | 0.61 | 0.88 | 25 | empty |
| 4 | 109 | 0.40 | 0.76 | 18 | EDO |
Compared structures
- 5U9D · Discovery of a potent BTK inhibitor with a novel binding mode using parallel selections… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q06187
- Elsewhere: RCSB PDB 5U9D · PDBe 5U9D · UniProt Q06187
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