MolNFT v1 · #151087 · protein
ABL1 in complex with COMPOUND6 and imatinib (sti-571)
6HD6 · Tyrosine-protein kinase ABL1: “ABL1 in complex with COMPOUND6 and imatinib (sti-571)”. X-ray diffraction, 3 ligands (STI, FYH, CL), 7 pockets (best druggability 0.78). MolNFT v1 #151087 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HD6
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ABL1
- EC
- 2.7.10.2
- UniProt
- P00520
- Ligands
- STI, FYH, CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 285 | 42% helix, 16% strand | P00520 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 283 | 41% helix, 16% strand | P00520 |
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 · 2 copies · chains A, B
- FYH · 3-(morpholin-4-ylmethyl)-~{N}-[4-(trifluoromethyloxy) phenyl]benzamide · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.78 | 0.80 | 59 | empty |
| 2 | 644 | 0.77 | 0.82 | 64 | STI |
| 3 | 640 | 0.75 | 0.81 | 66 | STI |
| 4 | 104 | 0.64 | 0.88 | 21 | empty |
| 5 | 106 | 0.60 | 0.86 | 21 | FYH |
Interfaces
1 interface between chains.
- A–B · 501 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P00520
- Elsewhere: RCSB PDB 6HD6 · PDBe 6HD6 · UniProt P00520
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