MolNFT v2 · #146075 · protein
Crystal Structure of KDM4A with Compound 8
6CG2 · Lysine-specific demethylase 4A: “Crystal Structure of KDM4A with Compound 8”. X-ray diffraction at 2.34, 3 ligands (QC2, NI, ZN), 20 pockets (best druggability 0.75). MolNFT v2 #146075 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CG2
- Type
- protein
- Length
- 1,368 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.34
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- QC2, NI, ZN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.34 · 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 | 345 | 31% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 347 | 31% helix, 24% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 335 | 33% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 341 | 29% helix, 25% strand | O75164 |
Ligands and binding sites
- QC2 · 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.75 | 0.79 | 85 | QC2 |
| 2 | 765 | 0.75 | 0.79 | 71 | NI, QC2 |
| 3 | 390 | 0.71 | 0.82 | 39 | NI, QC2 |
| 4 | 375 | 0.70 | 0.82 | 45 | NI, QC2 |
| 5 | 384 | 0.69 | 0.82 | 43 | empty |
Interfaces
3 interfaces between chains.
- C–D · 540 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6CG2 · Crystal structure of KDM4A with compound 8 · 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 6CG2 · PDBe 6CG2 · UniProt O75164
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