MolNFT v1 · #63534 · protein

Complex of UNG2 and a fragment-based designed inhibitor

3FCL · Uracil-DNA glycosylase: “Complex of UNG2 and a fragment-based designed inhibitor”. X-ray diffraction, 2 ligands (3FL, SCN), 3 pockets (best druggability 0.72). MolNFT v1 #63534 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3FCL
Type: protein
Length: 444 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uracil-DNA glycosylase
EC: 3.2.2.-
UniProt: P13051
Ligands: 3FL, SCN
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uracil-DNA glycosylase (EC 3.2.2.-)	protein	222	40% helix, 11% strand	P13051

Ligands and binding sites

3FL · 3-{[(4-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}butyl)amino]methyl}benzoic acid · ligand · 2 copies · chains A, B
SCN · Thiocyanate ion · ion · 8 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	579	0.72	0.80	47	3FL, SCN
2	60	0.59	0.90	16	SCN
3	112	0.52	0.82	29	3FL

Interfaces

1 interface between chains.

A–B · 543 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3FCL · Complex of UNG2 and a fragment-based designed inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · 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 P13051
Elsewhere: RCSB PDB 3FCL · PDBe 3FCL · UniProt P13051

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