MolNFT v1 · #39599 · protein
Human abl kinase domain in complex with imatinib (STI571, glivec)
2HYY · Proto-oncogene tyrosine-protein kinase ABL1: “Human abl kinase domain in complex with imatinib (STI571, glivec)”. X-ray diffraction, 1 ligand (STI), 15 pockets (best druggability 0.78). MolNFT v1 #39599 on GenesisL1: 3D structure…
- PDB
- 2HYY
- Type
- protein
- Length
- 1,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase ABL1
- EC
- 2.7.10.2
- UniProt
- P00519
- Ligands
- STI
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 263 | 43% helix, 17% strand | P00519 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 265 | 45% helix, 17% strand | P00519 |
| C | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 262 | 45% helix, 18% strand | P00519 |
| D | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 264 | 43% helix, 17% strand | P00519 |
Ligands and binding sites
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.78 | 0.83 | 68 | empty |
| 2 | 625 | 0.76 | 0.81 | 65 | STI |
| 3 | 651 | 0.74 | 0.80 | 63 | STI |
| 4 | 532 | 0.74 | 0.81 | 62 | STI |
| 5 | 507 | 0.71 | 0.80 | 55 | STI |
Interfaces
6 interfaces between chains.
- B–D · 527 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 520 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 453 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 360 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2HYY · Human Abl kinase domain in complex with imatinib (STI571, Glivec) · the same entry in another collection · chain D against D, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P00519
- Elsewhere: RCSB PDB 2HYY · PDBe 2HYY · UniProt P00519
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.