Research workbench
Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4- fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-PYRAZOLO[3,4- B]PYRIDIN-5-yl)-3-(TRIFLUOROMETHYL)BENZAMIDE
Analyse Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KWA
- Type
- protein
- Length
- 372 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOLYSIN,DCN1-like protein 1
- EC
- 3.2.1.17
- UniProt
- A0A097J809, Q96GG9
- Ligands
- YHP
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOLYSIN,DCN1-like protein 1 (EC 3.2.1.17) | protein | 372 | 62% helix, 8% strand | A0A097J809, Q96GG9 |
Ligands and binding sites
- YHP · N-[(4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]-3-(trifluoromethyl)benzamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.61 | 0.82 | 24 | YHP |
| 2 | 199 | 0.51 | 0.77 | 25 | empty |
| 3 | 269 | 0.50 | 0.74 | 39 | empty |
| 4 | 128 | 0.40 | 0.75 | 19 | empty |
Compared structures
- 7KWA · Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-p… · 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 0.58
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 A0A097J809
- Every structure of UniProt Q96GG9
- Elsewhere: RCSB PDB 7KWA · PDBe 7KWA · UniProt A0A097J809 · UniProt Q96GG9
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