MolNFT v1 · #118543 · protein

Crystal structure of human JMJD2D complexed with KDOAM16

5F5A · Lysine-specific demethylase 4D: “Crystal structure of human JMJD2D complexed with KDOAM16”. X-ray diffraction, 4 ligands (5V0, ZN, NI), 3 pockets (best druggability 0.76). MolNFT v1 #118543 on GenesisL1: 3D structure, binding sites…

PDB: 5F5A
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: 5V0, 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

5V0 · 2-[(furan-2-ylmethylamino)methyl]pyridine-4-carboxylic acid · 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 · 13 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	395	0.76	0.86	45	NI, 5V0
2	80	0.65	0.92	31	EDO
3	55	0.30	0.75	25	EDO

Compared structures

5F5A · Crystal Structure of human JMJD2D complexed with KDOAM16 · 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 5F5A · PDBe 5F5A · UniProt Q6B0I6

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