Research workbench
Abl kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket
Analyse Abl kinase in complex with imatinib and a fragment (FRAG1) in the myristate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MS9
- Type
- protein
- Length
- 537 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, MS9, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 265 | 44% helix, 17% strand | P00520 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 272 | 43% 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
- MS9 · methyl 2-amino-4-chlorobenzoate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.77 | 0.83 | 71 | STI, CL |
| 2 | 618 | 0.75 | 0.81 | 56 | STI, CL |
| 3 | 70 | 0.49 | 0.83 | 16 | MS9 |
| 4 | 68 | 0.47 | 0.83 | 16 | MS9 |
| 5 | 144 | 0.45 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3MS9 · ABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket · the same entry in another collection · chain A against A, TM-score 1.00
- P00520 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00520) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 3MS9 · PDBe 3MS9 · UniProt P00520
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