MolNFT v1 · #118479 · protein
Crystal structure of human KDM4A in complex with compound 40
5F32 · Lysine-specific demethylase 4A: “Crystal structure of human KDM4A in complex with compound 40”. X-ray diffraction, 2 ligands (5V7, ZN), 17 pockets (best druggability 0.75). MolNFT v1 #118479 on GenesisL1: 3D structure, binding sites…
- PDB
- 5F32
- Type
- protein
- Length
- 1,384 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
- 5V7, ZN
- Pockets
- 17 · best druggability 0.75
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 | 342 | 32% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 344 | 31% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 30% helix, 24% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 31% helix, 24% strand | O75164 |
Ligands and binding sites
- 5V7 · 8-(2-azanyl-1,3-thiazol-4-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 · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
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 | 909 | 0.75 | 0.78 | 74 | ZN, 5V7, DMS |
| 2 | 454 | 0.73 | 0.83 | 47 | ZN, 5V7, DMS |
| 3 | 421 | 0.72 | 0.83 | 44 | ZN, 5V7, DMS |
| 4 | 366 | 0.71 | 0.83 | 38 | ZN, 5V7, DMS |
| 5 | 575 | 0.70 | 0.79 | 62 | empty |
Interfaces
4 interfaces between chains.
- B–D · 501 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 38 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5F32 · Crystal structure of human KDM4A in complex with compound 40 · 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 5F32 · PDBe 5F32 · UniProt O75164
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