MolNFT v1 · #167950 · protein

Structure of khk in complex with compound 2

6W0N · Ketohexokinase: “Structure of khk in complex with compound 2”. X-ray diffraction, 2 ligands (RYS, SO4), 5 pockets (best druggability 0.77). MolNFT v1 #167950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W0N
Type: protein
Length: 597 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ketohexokinase
EC: 2.7.1.3
UniProt: P50053
Ligands: RYS, SO4
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ketohexokinase (EC 2.7.1.3)	protein	296	37% helix, 25% strand	P50053
B	Ketohexokinase (EC 2.7.1.3)	protein	301	36% helix, 25% strand	P50053

Ligands and binding sites

RYS · 6-[(3~{S},4~{R})-3,4-bis(oxidanyl)pyrrolidin-1-yl]-2-[(3~{S})-3-methyl-3-oxidanyl-pyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
CIT · Citric acid · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.77	0.83	64	RYS, SO4, CIT
2	730	0.73	0.79	71	RYS, SO4
3	63	0.53	0.87	23	empty
4	133	0.42	0.75	20	empty
5	72	0.38	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 1677 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6W0N · Structure of KHK in complex with compound 2 · the same entry in another collection · chain A against A, TM-score 1.00
P50053 · AlphaFold monomer V2.0 prediction for ketohexokinase (P50053) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P50053
Elsewhere: RCSB PDB 6W0N · PDBe 6W0N · UniProt P50053

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