MolNFT v1 · #160433 · protein
Inhibition of human menin by vtp-50469
6PKC · MENIN,MENIN: “Inhibition of human menin by vtp-50469”. X-ray diffraction, 1 ligand (OP4), 9 pockets (best druggability 0.78). MolNFT v1 #160433 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PKC
- Type
- protein
- Length
- 923 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MENIN,MENIN
- UniProt
- O00255
- Ligands
- OP4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MENIN,MENIN | protein | 462 | 56% helix, 5% strand | O00255 |
| B | MENIN,MENIN | protein | 461 | 58% helix, 5% strand | O00255 |
Ligands and binding sites
- OP4 · 5-fluoro-2-({4-[7-({trans-4-[(methylsulfonyl) amino]cyclohexyl}methyl)-2,7-diazaspiro[3.5]nonan-2-yl]pyrimidin-5-yl}oxy)-N,N-di(propan-2-yl)benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.78 | 0.80 | 87 | OP4 |
| 2 | 1053 | 0.77 | 0.79 | 90 | OP4 |
| 3 | 223 | 0.62 | 0.82 | 36 | empty |
| 4 | 241 | 0.55 | 0.78 | 34 | empty |
| 5 | 227 | 0.52 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1555 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 O00255
- Elsewhere: RCSB PDB 6PKC · PDBe 6PKC · UniProt O00255
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