MolNFT v1 · #169838 · protein

DCN1 bound to inhibitor 9

6XON · Lysozyme DCN1-like protein 1 chimera: “DCN1 bound to inhibitor 9”. X-ray diffraction, 1 ligand (H9M), 4 pockets (best druggability 0.69). MolNFT v1 #169838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XON
Type: protein
Length: 349 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme DCN1-like protein 1 chimera
EC: 3.2.1.17
UniProt: D9IEF7, Q96GG9
Ligands: H9M
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 62% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysozyme DCN1-like protein 1 chimera (EC 3.2.1.17)	protein	349	62% helix, 7% strand	D9IEF7, Q96GG9

Ligands and binding sites

H9M · (2S)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-4-(dimethylamino)-2-methylbutanamide · ligand · chains A

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

Pockets

4 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	185	0.69	0.86	26	H9M
2	377	0.58	0.76	48	empty
3	70	0.32	0.75	17	empty
4	63	0.28	0.73	13	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6XON · DCN1 bound to inhibitor 9 · 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 0.60

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 6XON · PDBe 6XON · UniProt D9IEF7 · UniProt Q96GG9

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