MolNFT v1 · #118491 · protein
Crystal structure of human KDM4A in complex with compound 54A
5F3E · Lysine-specific demethylase 4A: “Crystal structure of human KDM4A in complex with compound 54A”. X-ray diffraction, 2 ligands (5UO, ZN), 18 pockets (best druggability 0.72). MolNFT v1 #118491 on GenesisL1: 3D structure, binding…
- PDB
- 5F3E
- Type
- protein
- Length
- 1,347 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
- 5UO, ZN
- Pockets
- 18 · 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 | 337 | 31% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 335 | 30% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 340 | 33% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 335 | 30% helix, 25% strand | O75164 |
Ligands and binding sites
- 5UO · 8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]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
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.72 | 0.83 | 40 | ZN, 5UO |
| 2 | 379 | 0.70 | 0.82 | 41 | ZN, 5UO |
| 3 | 346 | 0.70 | 0.83 | 36 | ZN, 5UO |
| 4 | 351 | 0.70 | 0.82 | 35 | ZN, 5UO |
| 5 | 420 | 0.61 | 0.76 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–C · 519 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 314 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 53 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F3E · Crystal structure of human KDM4A in complex with compound 54a · 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 5F3E · PDBe 5F3E · UniProt O75164
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