MolNFT v1 · #136931 · protein

Structure of DCN1 bound to nacm-opt

5V86 · LYSOZYME,DCN1-like protein 1: “Structure of DCN1 bound to nacm-opt”. X-ray diffraction, 1 ligand (8ZA), 3 pockets (best druggability 0.65). MolNFT v1 #136931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V86
Type: protein
Length: 360 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LYSOZYME,DCN1-like protein 1
EC: 3.2.1.17
UniProt: D9IEF7, Q96GG9
Ligands: 8ZA
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LYSOZYME,DCN1-like protein 1 (EC 3.2.1.17)	protein	360	61% helix, 6% strand	D9IEF7, Q96GG9

Ligands and binding sites

8ZA · N-benzyl-N-(1-butylpiperidin-4-yl)-N'-(3,4-dichlorophenyl)urea · ligand · chains A

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	567	0.65	0.76	62	empty
2	143	0.59	0.83	24	8ZA
3	116	0.40	0.75	19	empty

Compared structures

5V86 · Structure of DCN1 bound to NAcM-OPT · the same entry in another collection · chain A against A, TM-score 1.00
Q96GG9 · AlphaFold monomer V2.0 prediction for DCN1-like protein 1 (Q96GG9) · a predicted model of the same protein · chain A against A, TM-score 0.57

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 D9IEF7
Every structure of UniProt Q96GG9
Elsewhere: RCSB PDB 5V86 · PDBe 5V86 · UniProt D9IEF7 · UniProt Q96GG9

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