MolNFT v1 · #118545 · protein
Crystal structure of human JMJD2D complexed with KDOPP7
5F5C · Lysine-specific demethylase 4D: “Crystal structure of human JMJD2D complexed with KDOPP7”. X-ray diffraction, 4 ligands (5V3, ZN, NI), 1 pocket (best druggability 0.75). MolNFT v1 #118545 on GenesisL1: 3D structure, binding sites…
- PDB
- 5F5C
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4D
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- 5V3, ZN, NI, SO4
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 330 | 32% helix, 26% strand | Q6B0I6 |
Ligands and binding sites
- 5V3 · 8-[[(phenylmethyl)amino]methyl]-1~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.75 | 0.84 | 51 | NI, 5V3 |
Compared structures
- 5F5C · Crystal Structure of human JMJD2D complexed with KDOPP7 · 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 Q6B0I6
- Elsewhere: RCSB PDB 5F5C · PDBe 5F5C · UniProt Q6B0I6
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