MolNFT v1 · #187181 · protein

Crystal structure of inhibitor-bound galactokinase

7S4C: “Crystal structure of inhibitor-bound galactokinase”. X-ray diffraction, 4 ligands (V3V, GLA, NA), 6 pockets (best druggability 0.79). MolNFT v1 #187181 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7S4C
Type: protein
Length: 782 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactokinase
EC: 2.7.1.6
UniProt: P51570
Ligands: V3V, GLA, NA, PO4
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Galactokinase (EC 2.7.1.6)	protein	391	41% helix, 23% strand	P51570

Ligands and binding sites

V3V · 2-({(4R)-4-(2-chlorophenyl)-2-[(6-fluoro-1,3-benzoxazol-2-yl)amino]-6-methyl-1,4-dihydropyrimidine-5-carbonyl}amino)pyridine-4-carboxylic acid · ligand · 3 copies · chains A, B
GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B

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

Pockets

6 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	1052	0.79	0.81	75	empty
2	448	0.73	0.83	53	GLA, V3V, PO4
3	392	0.73	0.84	51	GLA, V3V, PO4
4	262	0.63	0.81	34	V3V
5	70	0.34	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 868 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7S4C · Crystal Structure of Inhibitor-bound Galactokinase · the same entry in another collection · chain A against A, TM-score 1.00
P51570 · AlphaFold monomer V2.0 prediction for galactokinase (P51570) · 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 P51570
Elsewhere: RCSB PDB 7S4C · PDBe 7S4C · UniProt P51570

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