MolNFT v1 · #136971 · protein
Crystal structure of selective pyrrolidine amide KDM5A inhibitor N- {(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-CARBONYL]PYRROLIDIN-3- YL}CYCLOPROPANECARBOXAMIDE (compound 48)
5V9T · Lysine-specific demethylase 5A: “Crystal structure of selective pyrrolidine amide KDM5A inhibitor N…”. X-ray diffraction, 3 ligands (90V, ZN, NI), 18 pockets (best druggability 0.79). MolNFT v1 #136971 on GenesisL1: 3D structure…
- PDB
- 5V9T
- Type
- protein
- Length
- 1,180 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- 90V, ZN, NI
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 577 | 41% helix, 15% strand | P29375 |
| B | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 593 | 41% helix, 15% strand | P29375 |
| G | Lysine-specific demethylase 5A | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- 90V · N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.79 | 0.81 | 88 | 90V |
| 2 | 1137 | 0.79 | 0.80 | 89 | 90V |
| 3 | 164 | 0.76 | 0.93 | 23 | empty |
| 4 | 155 | 0.75 | 0.93 | 25 | empty |
| 5 | 677 | 0.73 | 0.79 | 78 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1272 Ų buried · 18 hydrogen bonds · protein-protein
- B–G · 271 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 139 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5V9T · Crystal structure of selective pyrrolidine amide KDM5a inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 5V9T · PDBe 5V9T · UniProt P29375
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