MolNFT v2 · #175640 · protein

Allene-Based Design of a Noncalcemic Vitamin D Receptor Agonist

7B39 · Vitamin D3 receptor A: “Allene-Based Design of a Noncalcemic Vitamin D Receptor Agonist”. X-ray diffraction at 2.13, 1 ligand (T0H), 3 pockets (best druggability 0.86). MolNFT v2 #175640 on GenesisL1: 3D structure, binding sites and…

PDB: 7B39
Type: protein
Length: 251 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.13
Source: Danio rerio; SYNTHETIC CONSTRUCT
Molecule: Vitamin D3 receptor A; Nuclear receptor coactivator 1
EC: 2.3.1.48
UniProt: Q9PTN2, Q15788
Ligands: T0H
Pockets: 3 · best druggability 0.86

Structure

x-ray diffraction · resolution 2.13 · 2 distinct chains · 68% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor A	protein	240	68% helix, 3% strand	Q9PTN2
B	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	11	64% helix, 0% strand	Q15788

Ligands and binding sites

T0H · (1R,3S,Z)-5-(2-((3aS,7aS,E)-1-(6-hydroxy-6-methylhept-1-en-1-ylidene)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-4-methylenecyclohexane-1,3-diol · ligand · chains A
ACT · Acetate ion · additive · 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	315	0.86	0.95	38	T0H, ACT
2	225	0.55	0.78	30	empty
3	63	0.33	0.76	10	empty

Interfaces

1 interface between chains.

A–B · 644 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7B39 · Allene-based design of a noncalcemic vitamin D receptor agonist · the same entry in another collection · chain A against A, TM-score 1.00
Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9PTN2
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 7B39 · PDBe 7B39 · UniProt Q9PTN2 · UniProt Q15788

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.