MolNFT v1 · #164589 · protein

Vdr-ZK168281 complex

6T2M · Vitamin D3 receptor a: “Vdr-ZK168281 complex”. X-ray diffraction, 1 ligand (M9Q), 2 pockets (best druggability 0.86). MolNFT v1 #164589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T2M
Type: protein
Length: 249 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor a; Nuclear receptor coactivator 1
EC: 2.3.1.48
UniProt: Q9PTN2, Q15788
Ligands: M9Q
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor a	protein	239	65% helix, 3% strand	Q9PTN2
B	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	10	60% helix, 0% strand	Q15788

Ligands and binding sites

M9Q · Ethyl (~{Z})-3-[1-[(~{E},1~{R},4~{R})-4-[(1~{R}, 3~{A}~{S},4~{E},7~{A}~{R})-7~{A}-methyl-4-[(2~{Z})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl) cyclohexylidene]ethylidene]-2,3,3~{A},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-oxidanyl-pent-2-enyl]cyclopropyl]prop-2-enoate · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	377	0.86	0.94	47	M9Q
2	180	0.48	0.76	31	empty

Interfaces

1 interface between chains.

A–B · 610 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6T2M · VDR-ZK168281 complex · 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 6T2M · PDBe 6T2M · UniProt Q9PTN2 · UniProt Q15788

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