Research workbench
Structure of 4-(4-tert-butylbenzyl)-1-(7H-PYRROLO(2,3-D) pyrimidin-4-YL)PIPERIDIN-4-amine bound to pkb
Analyse Structure of 4-(4-tert-butylbenzyl)-1-(7H-PYRROLO(2,3-D)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XH5
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rac-beta SERINE/THREONINE-protein kinase; Glycogen synthase kinase-3 beta
- EC
- 2.7.11.1, 2.7.11.26
- UniProt
- P31751, P49841
- Ligands
- X37
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rac-beta SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 317 | 35% helix, 17% strand | P31751 |
| C | Glycogen synthase kinase-3 beta (EC 2.7.11.26) | protein | 10 | 0% helix, 20% strand | P49841 |
Ligands and binding sites
- X37 · 4-(4-tert-butylbenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.80 | 0.85 | 51 | X37 |
| 2 | 115 | 0.40 | 0.75 | 17 | empty |
| 3 | 77 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 652 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2XH5 · Structure of 4-(4-tert-Butylbenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin-4- yl)piperidin-4-amine… · the same entry in another collection · chain A against A, TM-score 1.00
- P31751 · AlphaFold monomer V2.0 prediction for rac-beta SERINE/THREONINE- protein kinase (P31751) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P31751
- Every structure of UniProt P49841
- Elsewhere: RCSB PDB 2XH5 · PDBe 2XH5 · UniProt P31751 · UniProt P49841
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