MolNFT v1 · #179401 · protein

Cryo-EM structure of human TRPV6 in complex with (4- PHENYLCYCLOHEXYL)PIPERAZINE inhibitor 30

7K4E · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of human TRPV6 in complex with (4- PHENYLCYCLOHEXYL)PIPERAZINE inhibitor 30”. Electron microscopy, 1 ligand (VUJ), 20 pockets (best druggability 0.86).…

PDB: 7K4E
Type: protein
Length: 2,480 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 6
UniProt: Q9H1D0
Ligands: VUJ
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 53% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 6	protein	620	53% helix, 4% strand	Q9H1D0

Ligands and binding sites

VUJ · 5-({4-[(1R,4S)-3'-methyl[1,2,3,4-tetrahydro[1,1'-biphenyl]]-4-yl]piperazin-1-yl}methyl)pyridin-2(1H)-one · ligand · 5 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	538	0.86	0.92	59	empty
2	335	0.78	0.88	29	VUJ
3	59	0.71	0.97	18	empty
4	424	0.70	0.81	44	VUJ
5	426	0.70	0.81	42	VUJ

Interfaces

6 interfaces between chains.

A–B · 3492 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 3490 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 3478 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 3470 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 33 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7K4E · Cryo-EM structure of human TRPV6 in complex with (4- phenylcyclohexyl)piperazine… · the same entry in another collection · chain A against A, TM-score 1.00
Q9H1D0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · 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 Q9H1D0
Elsewhere: RCSB PDB 7K4E · PDBe 7K4E · UniProt Q9H1D0

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