MolNFT v1 · #168584 · protein

Cocomplex structure of deoxyhypusine synthase with inhibitor 6-[(1R)- 2-amino-1-phenylethyl]-3-(pyridin-3-yl)-4H,5H,6H,7H-THIENO[2,3- C]PYRIDIN-7-one

6WKZ: “Cocomplex structure of deoxyhypusine synthase with inhibitor 6-[(1R)…”. X-ray diffraction, 1 ligand (8Y1), 6 pockets (best druggability 0.88). MolNFT v1 #168584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WKZ
Type: protein
Length: 590 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: 8Y1
Pockets: 6 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyhypusine synthase (EC 2.5.1.46)	protein	294	49% helix, 13% strand	P49366
B	Deoxyhypusine synthase (EC 2.5.1.46)	protein	296	49% helix, 13% strand	P49366

Ligands and binding sites

8Y1 · 6-[(1R)-2-amino-1-phenylethyl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one · ligand · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	984	0.88	0.89	113	8Y1
2	247	0.56	0.77	25	empty
3	142	0.41	0.74	27	empty
4	95	0.38	0.76	25	empty
5	50	0.37	0.81	16	empty

Interfaces

1 interface between chains.

A–B · 2082 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6WKZ · 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 0.99

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

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