MolNFT v1 · #118489 · protein
Crystal structure of human KDM4A in complex with compound 52D
5F3C · Lysine-specific demethylase 4A: “Crystal structure of human KDM4A in complex with compound 52D”. X-ray diffraction, 3 ligands (5U8, ZN, CL), 17 pockets (best druggability 0.72). MolNFT v1 #118489 on GenesisL1: 3D structure, binding…
- PDB
- 5F3C
- Type
- protein
- Length
- 1,361 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- 5U8, ZN, CL
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 343 | 31% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 337 | 30% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 340 | 31% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 341 | 31% helix, 25% strand | O75164 |
Ligands and binding sites
- 5U8 · 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
- DMS · Dimethyl sulfoxide · additive · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.72 | 0.83 | 38 | 5U8 |
| 2 | 498 | 0.72 | 0.81 | 43 | ZN, 5U8 |
| 3 | 445 | 0.72 | 0.82 | 42 | ZN, 5U8, DMS |
| 4 | 423 | 0.72 | 0.82 | 40 | ZN, 5U8 |
| 5 | 409 | 0.62 | 0.76 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–D · 527 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 127 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5F3C · Crystal structure of human KDM4A in complex with compound 52d · the same entry in another collection · chain A 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 O75164
- Elsewhere: RCSB PDB 5F3C · PDBe 5F3C · UniProt O75164
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