MolNFT v1 · #171796 · protein

Structure of human galactokinase 1 bound with (4-CHLOROPHENYL)METHYL pyridine-3-carboxylate

6ZGW: “Structure of human galactokinase 1 bound with (4-CHLOROPHENYL)METHYL pyridine-3-carboxylate”. X-ray diffraction, 3 ligands (HFK, QKW, GAL), 15 pockets (best druggability 0.84). MolNFT v1 #171796 on GenesisL1: 3D structure, binding…

PDB: 6ZGW
Type: protein
Length: 1,543 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactokinase
EC: 2.7.1.6
UniProt: P51570
Ligands: HFK, QKW, GAL
Pockets: 15 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Galactokinase (EC 2.7.1.6)	protein	391	41% helix, 23% strand	P51570
B	Galactokinase (EC 2.7.1.6)	protein	390	42% helix, 23% strand	P51570
D	Galactokinase (EC 2.7.1.6)	protein	371	44% helix, 25% strand	P51570

Ligands and binding sites

HFK · 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one · ligand · 3 copies · chains A, B, E
QKW · (4-chlorophenyl)methyl pyridine-3-carboxylate · ligand · chains D
GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, E

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.84	0.86	73	empty
2	910	0.83	0.85	72	empty
3	415	0.77	0.87	52	GAL, HFK
4	859	0.77	0.80	76	empty
5	433	0.76	0.86	53	GAL, HFK

Interfaces

5 interfaces between chains.

A–B · 1047 Å² buried · 15 hydrogen bonds · protein-protein
E–D · 958 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 325 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 316 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 242 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 glycan (disulfide, glycosylation).

Compared structures

6ZGW · Structure of human galactokinase 1 bound with (4-chlorophenyl)methyl… · the same entry in another collection · chain D against D, TM-score 1.00
P51570 · AlphaFold monomer V2.0 prediction for galactokinase (P51570) · a predicted model of the same protein · chain E against A, TM-score 1.00

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 P51570
Elsewhere: RCSB PDB 6ZGW · PDBe 6ZGW · UniProt P51570

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