Research workbench
Crystal structure of the C-abl kinase domain in complex with PD173955
Analyse Crystal structure of the C-abl kinase domain in complex with PD173955 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M52
- Type
- protein
- Length
- 543 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase ABL1
- EC
- 2.7.1.112
- UniProt
- P00520
- Ligands
- P17
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.1.112) | protein | 271 | 42% helix, 18% strand | P00520 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.1.112) | protein | 272 | 44% helix, 18% strand | P00520 |
Ligands and binding sites
- P17 · 6-(2,6-dichloro-phenyl)-8-methyl-2-(3-methylsulfanyl-phenylamino)-8H-pyrido[2,3-d]pyrimidin-7-one · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.74 | 0.91 | 23 | P17 |
| 2 | 231 | 0.69 | 0.85 | 35 | P17 |
| 3 | 281 | 0.53 | 0.75 | 36 | empty |
| 4 | 230 | 0.49 | 0.74 | 32 | empty |
| 5 | 83 | 0.49 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1M52 · Crystal Structure of the c-Abl Kinase domain in complex with PD173955 · 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 0.96
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 1M52 · PDBe 1M52 · UniProt P00520
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