MolNFT v1 · #156346 · protein
Crystal structure of RNase L in complex with sunitinib
6M11 · Ribonuclease L: “Crystal structure of RNase L in complex with sunitinib”. X-ray diffraction, 3 ligands (25A, B49, PO4), 19 pockets (best druggability 0.79). MolNFT v1 #156346 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6M11
- Type
- protein
- Length
- 1,365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- 25A, B49, PO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Ribonuclease L | protein | 681 | 51% helix, 7% strand | A5H025 |
| b | Ribonuclease L | protein | 684 | 50% helix, 8% strand | A5H025 |
Ligands and binding sites
- 25A · 5'-O-monophosphoryladenylyl(2'->5')adenylyl(2'->5') adenosine · ligand · 2 copies · chains a, b
- B49 · N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.79 | 0.82 | 93 | empty |
| 2 | 903 | 0.74 | 0.78 | 81 | 25A |
| 3 | 1144 | 0.72 | 0.76 | 93 | 25A |
| 4 | 815 | 0.71 | 0.77 | 79 | empty |
| 5 | 287 | 0.64 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- a–b · 3813 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 6M11 · Crystal structure of Rnase L in complex with Sunitinib · 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 6M11 · PDBe 6M11 · UniProt A5H025
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