MolNFT v1 · #186004 · protein
GCN2 (EIF2ALPHA kinase 4, E2AK4) in complex with compound 1 (dovitinib)
7QQ6 · Eif-2-alpha kinase GCN2: “GCN2 (EIF2ALPHA kinase 4, E2AK4) in complex with compound 1 (dovitinib)”. X-ray diffraction, 1 ligand (38O), 15 pockets (best druggability 0.76). MolNFT v1 #186004 on GenesisL1: 3D structure, binding sites…
- PDB
- 7QQ6
- Type
- protein
- Length
- 1,071 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eif-2-alpha kinase GCN2
- EC
- 2.7.11.1
- UniProt
- Q9P2K8
- Ligands
- 38O
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eif-2-alpha kinase GCN2 (EC 2.7.11.1) | protein | 269 | 35% helix, 19% strand | Q9P2K8 |
| B | Eif-2-alpha kinase GCN2 (EC 2.7.11.1) | protein | 275 | 33% helix, 19% strand | Q9P2K8 |
| C | Eif-2-alpha kinase GCN2 (EC 2.7.11.1) | protein | 267 | 36% helix, 19% strand | Q9P2K8 |
| D | Eif-2-alpha kinase GCN2 (EC 2.7.11.1) | protein | 260 | 37% helix, 20% strand | Q9P2K8 |
Ligands and binding sites
- 38O · 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.76 | 0.81 | 83 | empty |
| 2 | 513 | 0.67 | 0.78 | 58 | empty |
| 3 | 248 | 0.64 | 0.81 | 38 | 38O |
| 4 | 289 | 0.63 | 0.80 | 35 | 38O |
| 5 | 282 | 0.63 | 0.80 | 39 | 38O |
Interfaces
4 interfaces between chains.
- A–D · 1016 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 977 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 785 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 421 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7QQ6 · GCN2 (EIF2ALPHA KINASE 4, E2AK4) IN COMPLEX WITH COMPOUND 1 (dovitinib) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9P2K8 · AlphaFold monomer V2.0 prediction for eif-2-alpha kinase GCN2 (Q9P2K8) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 Q9P2K8
- Elsewhere: RCSB PDB 7QQ6 · PDBe 7QQ6 · UniProt Q9P2K8
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