Research workbench

Bay-707 in complex with MTH1

Analyse Bay-707 in complex with MTH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NHY
Type: protein
Length: 306 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 7,8-dihydro-8-oxoguanine triphosphatase
EC: 3.6.1.55, 3.6.1.56
UniProt: P36639
Ligands: 8XT, SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56)	protein	154	16% helix, 47% strand	P36639
B	7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56)	protein	152	16% helix, 44% strand	P36639

Ligands and binding sites

8XT · ~{N}-ethyl-4-[(3~{S})-3-methylmorpholin-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine-2-carboxamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	269	0.72	0.86	33	8XT
2	240	0.72	0.86	35	8XT
3	70	0.31	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 470 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5NHY · BAY-707 in complex with MTH1 · the same entry in another collection · chain A against A, TM-score 1.00
P36639 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P36639) · 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 P36639
Elsewhere: RCSB PDB 5NHY · PDBe 5NHY · UniProt P36639

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