MolNFT v1 · #124842 · protein
KDM4C bound to pyrazolo-pyrimidine scaffold
5KR7 · Lysine-specific demethylase 4C: “KDM4C bound to pyrazolo-pyrimidine scaffold”. X-ray diffraction, 4 ligands (6X9, FE2, ZN), 6 pockets (best druggability 0.73). MolNFT v1 #124842 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5KR7
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4C
- EC
- 1.14.11.-
- UniProt
- Q9H3R0
- Ligands
- 6X9, FE2, ZN, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4C (EC 1.14.11.-) | protein | 340 | 31% helix, 25% strand | Q9H3R0 |
| B | Lysine-specific demethylase 4C (EC 1.14.11.-) | protein | 339 | 32% helix, 25% strand | Q9H3R0 |
Ligands and binding sites
- 6X9 · 6-ethyl-2,5-dimethyl-7-oxidanylidene-4~{H}-pyrazolo[1, 5-a]pyrimidine-3-carbonitrile · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.73 | 0.81 | 47 | FE2, 6X9 |
| 2 | 468 | 0.72 | 0.82 | 49 | 6X9 |
| 3 | 100 | 0.56 | 0.85 | 24 | empty |
| 4 | 100 | 0.51 | 0.82 | 25 | empty |
| 5 | 67 | 0.36 | 0.78 | 13 | empty |
Compared structures
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 Q9H3R0
- Elsewhere: RCSB PDB 5KR7 · PDBe 5KR7 · UniProt Q9H3R0
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