MolNFT v1 · #156348 · protein
Crystal structure of RNase L in complex with toceranib
6M13 · Ribonuclease L: “Crystal structure of RNase L in complex with toceranib”. X-ray diffraction, 3 ligands (BWC, 25L, PO4), 19 pockets (best druggability 0.79). MolNFT v1 #156348 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6M13
- Type
- protein
- Length
- 1,369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- BWC, 25L, PO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Ribonuclease L | protein | 681 | 49% helix, 7% strand | A5H025 |
| b | Ribonuclease L | protein | 688 | 48% helix, 7% strand | A5H025 |
Ligands and binding sites
- BWC · 5-[(Z)-(5-fluoranyl-2-oxidanylidene-1H-indol-3-ylidene)methyl]-2,4-dimethyl-N-(2-pyrrolidin-1-ylethyl)-1H-pyrrole-3-carboxamide · ligand · 2 copies · chains a, b
- 25L · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R, 5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate · ligand · 2 copies · chains a, b
- PO4 · Phosphate ion · ion · chains a, b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.79 | 0.82 | 84 | empty |
| 2 | 878 | 0.75 | 0.79 | 81 | 25L |
| 3 | 849 | 0.73 | 0.77 | 67 | 25L |
| 4 | 655 | 0.69 | 0.77 | 59 | empty |
| 5 | 210 | 0.63 | 0.83 | 33 | BWC |
Interfaces
1 interface between chains.
- a–b · 3670 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6M13 · Crystal structure of Rnase L in complex with Toceranib · 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 A5H025
- Elsewhere: RCSB PDB 6M13 · PDBe 6M13 · UniProt A5H025
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