Research workbench
Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1- phenyl-4-(P-tolyl)-4,5,6,7-tetrahydro-1H-PYRAZOLO[3,4-B]PYRIDIN-5- YL)BENZAMIDE
Analyse Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P5W
- Type
- protein
- Length
- 370 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
- O0A
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSOZYME,DCN1-like protein 1 chimera (EC 3.2.1.17) | protein | 370 | 63% helix, 7% strand | D9IEF7, Q96GG9 |
Ligands and binding sites
- O0A · 3-methyl-N-[(4S,5S)-3-methyl-4-(4-methylphenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.59 | 0.82 | 24 | O0A |
| 2 | 351 | 0.54 | 0.74 | 51 | empty |
| 3 | 103 | 0.45 | 0.79 | 18 | empty |
| 4 | 138 | 0.42 | 0.75 | 26 | empty |
Compared structures
- 6P5W · Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7… · 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 D9IEF7
- Every structure of UniProt Q96GG9
- Elsewhere: RCSB PDB 6P5W · PDBe 6P5W · UniProt D9IEF7 · UniProt Q96GG9
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