MolNFT v1 · #98674 · protein
Crystal structure of 1NM-PP1 bound to analog-sensitive src kinase
4LGH · Proto-oncogene tyrosine-protein kinase src: “Crystal structure of 1NM-PP1 bound to analog-sensitive src kinase”. X-ray diffraction, 1 ligand (0JN), 5 pockets (best druggability 0.66). MolNFT v1 #98674 on GenesisL1: 3D structure…
- PDB
- 4LGH
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- 0JN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 243 | 38% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 247 | 37% helix, 16% strand | P00523 |
Ligands and binding sites
- 0JN · 1-tert-butyl-3-(naphthalen-1-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 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 | 429 | 0.66 | 0.79 | 42 | 0JN |
| 2 | 271 | 0.61 | 0.80 | 31 | 0JN |
| 3 | 311 | 0.61 | 0.78 | 30 | empty |
| 4 | 187 | 0.47 | 0.75 | 40 | empty |
| 5 | 52 | 0.32 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4LGH · Crystal structure of 1NM-PP1 bound to analog-sensitive Src kinase · the same entry in another collection · chain A against A, TM-score 1.00
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 P00523
- Elsewhere: RCSB PDB 4LGH · PDBe 4LGH · UniProt P00523
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