MolNFT v1 · #135994 · protein

DCN1 bound to di-591

5UFI · DCN1-like protein 1: “DCN1 bound to di-591”. X-ray diffraction, 1 ligand (8B1), 5 pockets (best druggability 0.85). MolNFT v1 #135994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UFI
Type: protein
Length: 769 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DCN1-like protein 1
UniProt: Q96GG9
Ligands: 8B1
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	DCN1-like protein 1	protein	192	58% helix, 7% strand	Q96GG9
B	DCN1-like protein 1	protein	193	58% helix, 4% strand	Q96GG9

Ligands and binding sites

8B1 · N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl) propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide · ligand · 4 copies · chains A, C, B, D

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

Pockets

5 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	1050	0.85	0.85	85	8B1
2	1171	0.84	0.85	103	8B1
3	137	0.48	0.78	23	empty
4	118	0.45	0.78	24	empty
5	81	0.40	0.78	17	empty

Interfaces

3 interfaces between chains.

A–C · 723 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 712 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 609 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5UFI · DCN1 bound to DI-591 · the same entry in another collection · chain D against D, TM-score 1.00
Q96GG9 · AlphaFold monomer V2.0 prediction for DCN1-like protein 1 (Q96GG9) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q96GG9
Elsewhere: RCSB PDB 5UFI · PDBe 5UFI · UniProt Q96GG9

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