MolNFT v1 · #94943 · protein
Crystal structure of insulin receptor kinase domain in complex with an inhibitor irfin-1
4IBM: “Crystal structure of insulin receptor kinase domain in complex with an inhibitor irfin-1”. X-ray diffraction, 1 ligand (IR1), 8 pockets (best druggability 0.76). MolNFT v1 #94943 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4IBM
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin receptor
- EC
- 2.7.10.1
- UniProt
- P06213
- Ligands
- IR1
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin receptor (EC 2.7.10.1) | protein | 301 | 38% helix, 18% strand | P06213 |
| B | Insulin receptor (EC 2.7.10.1) | protein | 294 | 39% helix, 17% strand | P06213 |
Ligands and binding sites
- IR1 · 5-(2-phenylpyrazolo[1,5-a]pyridin-3-yl)-3H-pyrazolo[3,4-c]pyridazin-3-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.76 | 0.78 | 72 | empty |
| 2 | 668 | 0.74 | 0.80 | 63 | empty |
| 3 | 181 | 0.64 | 0.84 | 23 | IR1 |
| 4 | 159 | 0.63 | 0.85 | 25 | IR1 |
| 5 | 106 | 0.46 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4IBM · Crystal structure of insulin receptor kinase domain in complex with an inhibitor Irfin-1 · the same entry in another collection · chain A against A, TM-score 1.00
- P06213 · AlphaFold monomer V2.0 prediction for insulin receptor (P06213) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P06213
- Elsewhere: RCSB PDB 4IBM · PDBe 4IBM · UniProt P06213
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