MolNFT v1 · #123054 · protein
Discovery of N-(3-(5-((3-acrylamido-4-(morpholine-4-CARBONYL)PHENYL) amino)-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-2-methylphenyl)-4- (tert-BUTYL)BENZAMIDE (chmfl-btk-01) as a highly selective irreversible btk kinase inhibitor
5J87 · Tyrosine-protein kinase btk: “Discovery of N-(3-(5-((3-acrylamido-4-(morpholine-4-CARBONYL)PHENYL)…”. X-ray diffraction, 1 ligand (N42), 9 pockets (best druggability 0.79). MolNFT v1 #123054 on GenesisL1: 3D structure, binding sites…
- PDB
- 5J87
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- 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
- N42
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 263 | 42% helix, 16% strand | Q06187 |
| B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 274 | 42% helix, 17% strand | Q06187 |
| C | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 261 | 40% helix, 16% strand | Q06187 |
Ligands and binding sites
- N42 · N-[3-(5-{[3-(acryloylamino)-4-(morpholine-4-carbonyl)phenyl]amino}-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-2-methylphenyl]-4-tert-butylbenzamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.79 | 0.83 | 69 | empty |
| 2 | 821 | 0.74 | 0.78 | 88 | N42 |
| 3 | 651 | 0.71 | 0.79 | 70 | N42 |
| 4 | 328 | 0.69 | 0.82 | 40 | N42 |
| 5 | 389 | 0.66 | 0.79 | 50 | N42 |
Interfaces
4 interfaces between chains.
- C–D · 739 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 348 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 323 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5J87 · Discovery of N-(3-(5-((3-acrylamido-4-(morpholine-4-carbonyl)phenyl)amino)-1-methyl-6-oxo… · the same entry in another collection · chain D against D, 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 0.99
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 Q06187
- Elsewhere: RCSB PDB 5J87 · PDBe 5J87 · UniProt Q06187
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