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Crystal structure of the kinase domain of human TRAF2- and nck- interacting kinase with WEE1CHK1 inhibitor
Analyse Crystal structure of the kinase domain of human TRAF2- and nck- interacting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X7F
- Type
- protein
- Length
- 1,336 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRAF2 and nck-interacting protein kinase
- EC
- 2.7.11.1
- UniProt
- Q9UKE5
- Ligands
- 824, NA
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 276 | 42% helix, 18% strand | Q9UKE5 |
| B | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 288 | 42% helix, 17% strand | Q9UKE5 |
| C | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 285 | 41% helix, 18% strand | Q9UKE5 |
| D | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 236 | 45% helix, 13% strand | Q9UKE5 |
| E | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 251 | 39% helix, 17% strand | Q9UKE5 |
Ligands and binding sites
- 824 · 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione · ligand · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.79 | 0.81 | 102 | empty |
| 2 | 168 | 0.71 | 0.89 | 27 | 824 |
| 3 | 228 | 0.70 | 0.86 | 40 | 824 |
| 4 | 533 | 0.69 | 0.79 | 70 | 824 |
| 5 | 403 | 0.62 | 0.77 | 52 | 824 |
Interfaces
5 interfaces between chains.
- A–B · 472 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 379 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 378 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 43 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2X7F · Crystal structure of the kinase domain of human Traf2- and Nck- interacting Kinase with… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9UKE5 · AlphaFold monomer V2.0 prediction for TRAF2 and nck-interacting protein kinase (Q9UKE5) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q9UKE5
- Elsewhere: RCSB PDB 2X7F · PDBe 2X7F · UniProt Q9UKE5
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