Research workbench
Human abl kinase in complex with nilotinib
Analyse Human abl kinase in complex with nilotinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CS9
- Type
- protein
- Length
- 1,017 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
- NIL
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 264 | 45% helix, 17% strand | P00519 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 247 | 47% helix, 15% strand | P00519 |
| C | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 243 | 47% helix, 15% strand | P00519 |
| D | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 263 | 43% helix, 16% strand | P00519 |
Ligands and binding sites
- NIL · Nilotinib · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.82 | 0.83 | 75 | NIL |
| 2 | 446 | 0.73 | 0.83 | 65 | NIL |
| 3 | 299 | 0.72 | 0.85 | 41 | NIL |
| 4 | 342 | 0.71 | 0.83 | 43 | NIL |
| 5 | 641 | 0.64 | 0.74 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–B · 627 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 180 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 164 Ų buried · 2 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 P00519
- Elsewhere: RCSB PDB 3CS9 · PDBe 3CS9 · UniProt P00519
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