MolNFT v1 · #126200 · protein
Crystal structure of human pcaf bromodomain in complex with compound-D (cpd-D), N-methyl-2-(tetrahydro-2H-pyran-4-YLOXY)BENZAMIDE
5LVQ · Histone acetyltransferase KAT2B: “Crystal structure of human pcaf bromodomain in complex with compound-D (cpd-D)…”. X-ray diffraction, 1 ligand (2LX), 3 pockets (best druggability 0.66). MolNFT v1 #126200 on GenesisL1: 3D structure…
- PDB
- 5LVQ
- Type
- protein
- Length
- 216 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
- 2LX
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 108 | 63% helix, 0% strand | Q92831 |
| B | Histone acetyltransferase KAT2B (EC 2.3.1.48) | protein | 108 | 65% helix, 0% strand | Q92831 |
Ligands and binding sites
- 2LX · N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · 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 | 532 | 0.66 | 0.77 | 37 | empty |
| 2 | 103 | 0.55 | 0.84 | 19 | EDO, DMS |
| 3 | 97 | 0.53 | 0.83 | 21 | 2LX |
Interfaces
1 interface between chains.
- A–B · 684 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5LVQ · Crystal structure of human PCAF bromodomain in complex with compound-D (CPD-D)… · 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 B 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 5LVQ · PDBe 5LVQ · UniProt Q92831
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