MolNFT v1 · #119215 · protein
Crystal structure of human KDM4D in complex with 3H,4H- pyrido-3,4-D-pyrimidin-4-one
5FPA · Lysine-specific demethylase 4D: “Crystal structure of human KDM4D in complex with 3H,4H- pyrido-3,4-D-pyrimidin-4-one”. X-ray diffraction, 4 ligands (N5J, ZN, CO), 3 pockets (best druggability 0.74). MolNFT v1 #119215 on GenesisL1…
- PDB
- 5FPA
- Type
- protein
- Length
- 328 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
- N5J, ZN, CO, SO4
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 328 | 33% helix, 26% strand | Q6B0I6 |
Ligands and binding sites
- N5J · 3H-pyrido[3,4-d]pyrimidin-4-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CO · Cobalt (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.74 | 0.82 | 51 | CO, N5J, SO4 |
| 2 | 73 | 0.43 | 0.81 | 21 | empty |
| 3 | 67 | 0.31 | 0.74 | 26 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5FPA · Crystal structure of human KDM4D in complex with 3H,4H-pyrido-3,4-d- pyrimidin-4-one · 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 5FPA · PDBe 5FPA · UniProt Q6B0I6
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