MolNFT v1 · #160312 · protein

Cocomplex structure of deoxyhypusine synthase with inhibitor 6-bromo- N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide

6PGR: “Cocomplex structure of deoxyhypusine synthase with inhibitor 6-bromo…”. X-ray diffraction, 1 ligand (8XY), 7 pockets (best druggability 0.89). MolNFT v1 #160312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PGR
Type: protein
Length: 691 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyhypusine synthase
EC: 2.5.1.46
UniProt: P49366
Ligands: 8XY
Pockets: 7 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyhypusine synthase (EC 2.5.1.46)	protein	347	48% helix, 12% strand	P49366
B	Deoxyhypusine synthase (EC 2.5.1.46)	protein	344	47% helix, 12% strand	P49366

Ligands and binding sites

8XY · 6-bromo-N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1071	0.89	0.90	116	8XY
2	198	0.57	0.80	22	empty
3	173	0.55	0.80	26	empty
4	143	0.44	0.76	37	empty
5	67	0.33	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 3162 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

6PGR · Cocomplex structure of Deoxyhypusine synthase with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
P49366 · AlphaFold monomer V2.0 prediction for deoxyhypusine synthase (P49366) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P49366
Elsewhere: RCSB PDB 6PGR · PDBe 6PGR · UniProt P49366

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