MolNFT v1 · #168188 · protein

K2P2.1 (trek-1):ML335 complex, 100 mm K+

6W86 · Potassium channel subfamily K member 2: “K2P2.1 (trek-1):ML335 complex, 100 mm K+”. X-ray diffraction, 7 ligands (LNK, Q6F, D12), 14 pockets (best druggability 0.80). MolNFT v1 #168188 on GenesisL1: 3D structure, binding sites and…

PDB: 6W86
Type: protein
Length: 557 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potassium channel subfamily K member 2
UniProt: P97438
Ligands: LNK, Q6F, D12, R16, D10, K, CD
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Potassium channel subfamily K member 2	protein	276	78% helix, 0% strand	P97438
B	Potassium channel subfamily K member 2	protein	281	75% helix, 0% strand	P97438

Ligands and binding sites

LNK · Pentane · ligand · 3 copies · chains A, B
Q6F · N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl) amino]benzamide · ligand · 2 copies · chains A, B
D12 · Dodecane · ligand · 2 copies · chains A, B
R16 · Hexadecane · ligand · 2 copies · chains A, B
D10 · Decane · ligand · chains A, B
K · Potassium ion · metal · 5 copies · chains A, B
CD · Cadmium ion · metal · 3 copies · chains B
OCT · N-octane · additive · 4 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.80	0.84	98	CD, Q6F, K
2	198	0.71	0.87	35	Q6F
3	582	0.66	0.76	42	empty
4	77	0.53	0.85	16	empty
5	171	0.51	0.78	25	empty

Interfaces

1 interface between chains.

A–B · 5177 Å² buried · 49 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6W86 · K2P2.1 (TREK-1):ML335 complex, 100 mM K+ · the same entry in another collection · chain A against A, TM-score 1.00
P97438 · AlphaFold monomer V2.0 prediction for potassium channel subfamily K member 2 (P97438) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P97438
Elsewhere: RCSB PDB 6W86 · PDBe 6W86 · UniProt P97438

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