MolNFT v1 · #71324 · protein
Crystal structure of human HDAC2 complexed with an N-(2-aminophenyl) benzamide
3MAX · Histone deacetylase 2: “Crystal structure of human HDAC2 complexed with an N-(2-aminophenyl) benzamide”. X-ray diffraction, 4 ligands (LLX, ZN, CA), 7 pockets (best druggability 0.73). MolNFT v1 #71324 on GenesisL1: 3D structure…
- PDB
- 3MAX
- Type
- protein
- Length
- 1,097 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 2
- EC
- 3.5.1.98
- UniProt
- Q92769
- Ligands
- LLX, ZN, CA, NA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 2 (EC 3.5.1.98) | protein | 367 | 41% helix, 13% strand | Q92769 |
| B | Histone deacetylase 2 (EC 3.5.1.98) | protein | 364 | 41% helix, 13% strand | Q92769 |
| C | Histone deacetylase 2 (EC 3.5.1.98) | protein | 366 | 41% helix, 13% strand | Q92769 |
Ligands and binding sites
- LLX · N-(4-aminobiphenyl-3-yl)benzamide · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.73 | 0.78 | 72 | empty |
| 2 | 574 | 0.66 | 0.76 | 54 | empty |
| 3 | 87 | 0.63 | 0.90 | 27 | ZN, LLX |
| 4 | 95 | 0.62 | 0.88 | 32 | LLX |
| 5 | 88 | 0.62 | 0.89 | 27 | LLX |
Interfaces
3 interfaces between chains.
- A–C · 654 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 375 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3MAX · Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide · the same entry in another collection · chain A against A, TM-score 1.00
- Q92769 · AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q92769
- Elsewhere: RCSB PDB 3MAX · PDBe 3MAX · UniProt Q92769
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