MolNFT v1 · #121061 · protein

Human sigma-1 receptor bound to 4-ibp

5HK2 · Sigma non-opioid intracellular receptor 1: “Human sigma-1 receptor bound to 4-ibp”. X-ray diffraction, 2 ligands (61V, SO4), 8 pockets (best druggability 0.85). MolNFT v1 #121061 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5HK2
Type: protein
Length: 641 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sigma non-opioid intracellular receptor 1
UniProt: Q99720
Ligands: 61V, SO4
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sigma non-opioid intracellular receptor 1	protein	217	40% helix, 29% strand	Q99720
B	Sigma non-opioid intracellular receptor 1	protein	212	38% helix, 29% strand	Q99720
C	Sigma non-opioid intracellular receptor 1	protein	212	40% helix, 29% strand	Q99720

Ligands and binding sites

61V · N-(1-benzylpiperidin-4-yl)-4-iodobenzamide · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 12 copies · chains A, B, C
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 7 copies · chains B, C

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	246	0.85	0.97	37	61V
2	226	0.84	0.96	33	61V
3	229	0.84	0.96	34	61V
4	194	0.80	0.94	61	SO4
5	154	0.45	0.75	18	empty

Interfaces

3 interfaces between chains.

A–B · 1006 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1001 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 986 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5HK2 · Human sigma-1 receptor bound to 4-IBP · the same entry in another collection · chain A against A, TM-score 1.00
Q99720 · AlphaFold monomer V2.0 prediction for sigma non-opioid intracellular receptor 1 (Q99720) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q99720
Elsewhere: RCSB PDB 5HK2 · PDBe 5HK2 · UniProt Q99720

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