Research workbench
Crystal structure of bmp-2-inducible kinase in complex with an indazole inhibitor
Analyse Crystal structure of bmp-2-inducible kinase in complex with an indazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I3R
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bmp-2-inducible protein kinase
- EC
- 2.7.11.1
- UniProt
- Q9NSY1
- Ligands
- IDK, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bmp-2-inducible protein kinase (EC 2.7.11.1) | protein | 302 | 37% helix, 21% strand | Q9NSY1 |
Ligands and binding sites
- IDK · N-[6-(3-{[(cyclopropylmethyl)sulfonyl]amino}phenyl)-1H-indazol-3-yl]cyclopropanecarboxamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.77 | 0.82 | 62 | IDK |
| 2 | 457 | 0.73 | 0.82 | 52 | IDK |
| 3 | 187 | 0.52 | 0.78 | 26 | empty |
| 4 | 95 | 0.39 | 0.77 | 17 | empty |
| 5 | 96 | 0.38 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5I3R · Crystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NSY1 · AlphaFold monomer V2.0 prediction for bmp-2-inducible protein kinase (Q9NSY1) · a predicted model of the same protein · chain B 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 Q9NSY1
- Elsewhere: RCSB PDB 5I3R · PDBe 5I3R · UniProt Q9NSY1
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