Research workbench
1.68A structure pcaf bromodomain with 4-chloro-2-methyl-5- (METHYLAMINO)PYRIDAZIN-3(2H)-one
Analyse 1.68A structure pcaf bromodomain with 4-chloro-2-methyl-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MKX
- Type
- protein
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase KAT2B
- EC
- 2.3.1.48
- UniProt
- Q92831
- Ligands
- 82I, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 106 | 65% helix, 0% strand | Q92831 |
| B | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 107 | 67% helix, 0% strand | Q92831 |
Ligands and binding sites
- 82I · 4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- BU1 · 1,4-butanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.65 | 0.78 | 36 | empty |
| 2 | 103 | 0.51 | 0.82 | 17 | 82I |
| 3 | 77 | 0.50 | 0.84 | 20 | 82I |
Interfaces
1 interface between chains.
- A–B · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5MKX · 1.68A STRUCTURE PCAF BROMODOMAIN WITH 4-chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one · the same entry in another collection · chain A against A, TM-score 1.00
- Q92831 · AlphaFold monomer V2.0 prediction for histone acetyltransferase KAT2B (Q92831) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q92831
- Elsewhere: RCSB PDB 5MKX · PDBe 5MKX · UniProt Q92831
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