Research workbench
Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H- pyrazol-1-YL)PYRROLIDIN-1-YL][3-(propan-2-yl)-1H-pyrazol-5- YL]METHANONE (compound 35) in complex with KDM5A
Analyse Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V9P
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- 90S, ZN, NI, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 577 | 42% helix, 14% strand | P29375 |
| B | Lysine-specific demethylase 5A | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- 90S · [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.78 | 0.80 | 92 | NI, 90S, SO4 |
| 2 | 151 | 0.75 | 0.93 | 25 | empty |
| 3 | 68 | 0.52 | 0.86 | 19 | empty |
| 4 | 51 | 0.48 | 0.86 | 16 | empty |
| 5 | 117 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 147 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P29375
- Elsewhere: RCSB PDB 5V9P · PDBe 5V9P · UniProt P29375
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