MolNFT v1 · #118484 · protein
Crystal structure of human KDM4A in complex with compound 58
5F37 · Lysine-specific demethylase 4A: “Crystal structure of human KDM4A in complex with compound 58”. X-ray diffraction, 2 ligands (N5J, ZN), 18 pockets (best druggability 0.71). MolNFT v1 #118484 on GenesisL1: 3D structure, binding sites…
- PDB
- 5F37
- Type
- protein
- Length
- 1,403 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
- N5J, ZN
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 354 | 31% helix, 24% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 31% helix, 24% strand | O75164 |
Ligands and binding sites
- N5J · 3H-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
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B, C, D
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 | 425 | 0.71 | 0.82 | 47 | ZN, N5J, EDO |
| 2 | 380 | 0.70 | 0.82 | 49 | ZN, N5J, EDO |
| 3 | 343 | 0.69 | 0.82 | 39 | ZN, N5J, EDO |
| 4 | 402 | 0.68 | 0.81 | 40 | ZN, N5J, EDO |
| 5 | 553 | 0.68 | 0.78 | 61 | EDO |
Interfaces
3 interfaces between chains.
- B–D · 518 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 125 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5F37 · Crystal structure of human KDM4A in complex with compound 58 · 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 5F37 · PDBe 5F37 · UniProt O75164
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