MolNFT v1 · #146730 · protein
Linked KDM5A jmj domain bound to the potential hydrolysis product of inhibitor N45 I.E. 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4- diazepan-1-yl)-2-(pyridin-2-YL)PYRIMIDIN-4-YL)AMINO)PROPANOIC acid
6DQ7: “Linked KDM5A jmj domain bound to the potential hydrolysis product of inhibitor N45 I.E.…”. X-ray diffraction, 2 ligands (H6M, MN), 3 pockets (best druggability 0.67). MolNFT v1 #146730 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DQ7
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linked KDM5A jmj domain
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- H6M, MN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linked KDM5A jmj domain (EC 1.14.11.-) | protein | 294 | 29% helix, 23% strand | P29375 |
Ligands and binding sites
- H6M · N-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.67 | 0.80 | 44 | H6M, MN |
| 2 | 95 | 0.40 | 0.77 | 16 | empty |
| 3 | 55 | 0.40 | 0.81 | 18 | empty |
Compared structures
- 6DQ7 · LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF INHIBITOR N45 i.e.… · the same entry in another collection · chain A against A, TM-score 1.00
- P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P29375
- Elsewhere: RCSB PDB 6DQ7 · PDBe 6DQ7 · UniProt P29375
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