MolNFT v1 · #148411 · protein
Crystal structure of KDM4D with tetrazole ligand GF057
6F5T · Lysine-specific demethylase 4D: “Crystal structure of KDM4D with tetrazole ligand GF057”. X-ray diffraction, 4 ligands (CQK, ZN, NI), 3 pockets (best druggability 0.76). MolNFT v1 #148411 on GenesisL1: 3D structure, binding sites…
- PDB
- 6F5T
- 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
- CQK, ZN, NI, SO4
- Pockets
- 3 · best druggability 0.76
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 | 330 | 33% helix, 26% strand | Q6B0I6 |
Ligands and binding sites
- CQK · ~{N}-oxidanyl-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 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 | 568 | 0.76 | 0.83 | 63 | NI, CQK |
| 2 | 61 | 0.35 | 0.78 | 17 | empty |
| 3 | 56 | 0.29 | 0.74 | 19 | EDO |
Compared structures
- 6F5T · Crystal Structure of KDM4D with tetrazole ligand GF057 · 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 6F5T · PDBe 6F5T · UniProt Q6B0I6
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