Research workbench

Human gkrp bound to amg-2668

Analyse Human gkrp bound to amg-2668 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OHO
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: 2TG, S6P, IOD, SO4
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	52% helix, 11% strand	Q14397
B	Glucokinase regulatory protein	protein	590	53% helix, 11% strand	Q14397

Ligands and binding sites

2TG · 5-{[(3S)-3-(prop-1-yn-1-yl)-4-{4-[S-(trifluoromethyl)sulfonimidoyl]phenyl}piperazin-1-yl]sulfonyl}pyridin-2-amine · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
IOD · Iodide ion · ion · 25 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains B
GOL · Glycerol · additive · chains B

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.79	0.95	35	S6P
2	459	0.78	0.86	42	2TG, IOD
3	460	0.76	0.85	41	2TG, IOD
4	289	0.76	0.89	60	S6P, IOD, GOL
5	716	0.74	0.80	79	empty

Interfaces

1 interface between chains.

A–B · 703 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

4OHO · Human GKRP bound to AMG-2668 · 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 4OHO · PDBe 4OHO · UniProt Q14397

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