MolNFT v1 · #102544 · protein

Gkrp bound to AMG0556 and sorbitol-6-phosphate

4OP1 · Glucokinase regulatory protein: “Gkrp bound to AMG0556 and sorbitol-6-phosphate”. X-ray diffraction, 4 ligands (2UW, S6P, IOD), 13 pockets (best druggability 0.83). MolNFT v1 #102544 on GenesisL1: 3D structure, binding sites and…

PDB: 4OP1
Type: protein
Length: 1,175 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucokinase regulatory protein
UniProt: Q14397
Ligands: 2UW, S6P, IOD, SO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	53% helix, 11% strand	Q14397
B	Glucokinase regulatory protein	protein	590	54% helix, 11% strand	Q14397

Ligands and binding sites

2UW · (2S)-2-(6-{5-[(6-aminopyridin-3-yl)sulfonyl]thiophen-2-yl}-5-chloropyridin-3-yl)-1,1,1-trifluoropropan-2-ol · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
IOD · Iodide ion · ion · 28 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains B
GOL · Glycerol · additive · chains B

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	779	0.83	0.86	101	2UW, S6P, IOD, GOL
2	604	0.83	0.88	82	2UW, S6P, IOD
3	889	0.75	0.79	100	IOD
4	215	0.56	0.79	29	IOD
5	104	0.56	0.84	24	IOD

Interfaces

1 interface between chains.

A–B · 674 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4OP1 · GKRP bound to AMG0556 and Sorbitol-6-Phosphate · the same entry in another collection · chain A against A, TM-score 1.00
Q14397 · AlphaFold monomer V2.0 prediction for glucokinase regulatory protein (Q14397) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q14397
Elsewhere: RCSB PDB 4OP1 · PDBe 4OP1 · UniProt Q14397

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