MolNFT v1 · #158174 · protein
Crystal structure of SAM-bound PRDM9 in complex with mrk-740 inhibitor
6NM4 · Histone-lysine N-methyltransferase PRDM9: “Crystal structure of SAM-bound PRDM9 in complex with mrk-740 inhibitor”. X-ray diffraction, 4 ligands (SAM, KS7, ZN), 6 pockets (best druggability 0.60). MolNFT v1 #158174 on GenesisL1: 3D…
- PDB
- 6NM4
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase PRDM9
- EC
- 2.1.1.43
- UniProt
- Q9NQV7
- Ligands
- SAM, KS7, ZN, UNX
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 185 | 13% helix, 34% strand | Q9NQV7 |
| B | Histone-lysine N-methyltransferase PRDM9 (EC 2.1.1.43) | protein | 183 | 13% helix, 33% strand | Q9NQV7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- KS7 · 4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.60 | 0.81 | 29 | SAM, KS7 |
| 2 | 114 | 0.49 | 0.81 | 20 | UNX |
| 3 | 117 | 0.42 | 0.76 | 23 | empty |
| 4 | 57 | 0.37 | 0.79 | 18 | empty |
| 5 | 74 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 724 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6NM4 · Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NQV7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase PRDM9 (Q9NQV7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9NQV7
- Elsewhere: RCSB PDB 6NM4 · PDBe 6NM4 · UniProt Q9NQV7
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