Download MendeleyDiscovery of Novel LSD1 Inhibitors for the Treatment of Autosomal Dominant Polycystic Kidney Disease
Jiang, H., Tongchao, L., Bing, X., Zhiyan, D., Danyan, C.To be published.
8YM7
Crystal structure of Lysine Specific Demethylase 1 (LSD1) with JH-45
- PDB DOI: https://doi.org/10.2210/pdb8YM7/pdb
- Classification: FLAVOPROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-03-08 Released: 2024-05-22
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.83 Å
- R-Value Free: 0.248
- R-Value Work: 0.212
- R-Value Observed: 0.213
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lysine-specific histone demethylase 1A | 660 | Homo sapiens | Mutation(s): 0 Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1.14.99.66 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O60341 (Homo sapiens) Explore O60341 Go to UniProtKB: O60341 | |||||
PHAROS: O60341 GTEx: ENSG00000004487 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O60341 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| REST corepressor 1 | 134 | Homo sapiens | Mutation(s): 0 Gene Names: RCOR1, KIAA0071, RCOR |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0 Go to UniProtKB: Q9UKL0 | |||||
PHAROS: Q9UKL0 GTEx: ENSG00000089902 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UKL0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FAD (Subject of Investigation/LOI) Query on FAD | C [auth A] | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | ||
| A1LZJ (Subject of Investigation/LOI) Query on A1LZJ | D [auth A] | 4-[5-(4-azanylpiperidin-1-yl)-8-(4-methylphenyl)pyrido[3,4-b]pyrazin-7-yl]-2-fluoranyl-benzenecarbonitrile C26 H23 F N6 BISBXLFNGMDQKO-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.83 Å
- R-Value Free: 0.248
- R-Value Work: 0.212
- R-Value Observed: 0.213
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 120.674 | α = 90 |
| b = 178.038 | β = 90 |
| c = 234.346 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-05-22 Deposition Author(s): Zhiyan, D., Danyan, C., Hong, J., Tongchao, L., Bing, X.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-05-22
Type: Initial release
