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Crystal structure of cyclin-G associated kinase (gak) complexed with selective 12I inhibitor
Analyse Crystal structure of cyclin-G associated kinase (gak) complexed with selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y8D
- Type
- protein
- Length
- 765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-G-associated kinase; Nanobody
- EC
- 2.7.11.1
- UniProt
- O14976
- Ligands
- 49J
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclin-G-associated kinase (EC 2.7.11.1) | protein | 262 | 36% helix, 21% strand | O14976 |
| C | Nanobody | protein | 120 | 8% helix, 48% strand | — |
| D | Nanobody | protein | 121 | 8% helix, 47% strand | — |
Ligands and binding sites
- 49J · 2-methoxy-4-[3-(morpholin-4-yl)[1,2]thiazolo[4,3-b]pyridin-6-yl]aniline · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.68 | 0.77 | 62 | empty |
| 2 | 656 | 0.68 | 0.77 | 59 | empty |
| 3 | 312 | 0.64 | 0.80 | 37 | 49J |
| 4 | 259 | 0.61 | 0.80 | 29 | 49J |
| 5 | 100 | 0.58 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1505 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 653 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 642 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4Y8D · Crystal structure of Cyclin-G associated kinase (GAK) complexed with selective 12i… · the same entry in another collection · chain A against A, TM-score 1.00
- O14976 · AlphaFold monomer V2.0 prediction for cyclin-G-associated kinase (O14976) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O14976
- Elsewhere: RCSB PDB 4Y8D · PDBe 4Y8D · UniProt O14976
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