Research workbench
Structure of (3S,4S)-1-benzyl-4-(3-(3-(TRIFLUOROMETHYL)PHENYL)UREIDO) piperidin-3-yl acetate bound to DCN1
Analyse Structure of (3S,4S)-1-benzyl-4-(3-(3-(TRIFLUOROMETHYL)PHENYL)UREIDO)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BG3
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endolysin, DCN1-like protein 1 chimera
- EC
- 3.2.1.17
- UniProt
- P00720, Q96GG9
- Ligands
- DOJ
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endolysin, DCN1-like protein 1 chimera (EC 3.2.1.17) | protein | 366 | 61% helix, 8% strand | P00720, Q96GG9 |
Ligands and binding sites
- DOJ · N-{(3S,4S)-1-benzyl-3-[(1S)-1-hydroxyethoxy]piperidin-4-yl}-N'-[3-(trifluoromethyl)phenyl]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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.63 | 0.76 | 56 | empty |
| 2 | 136 | 0.62 | 0.85 | 23 | DOJ |
| 3 | 145 | 0.43 | 0.75 | 25 | empty |
Compared structures
- 6BG3 · Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl… · 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 P00720
- Every structure of UniProt Q96GG9
- Elsewhere: RCSB PDB 6BG3 · PDBe 6BG3 · UniProt P00720 · UniProt Q96GG9
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