Download Mendeleyco-crystal structure of non-carboxylic acid inhibitor with PHD2
Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Man, Z., Ding, X., Ren, F., Zhavoronkov, A.To be published.
8J1K
co-crystal structure of non-carboxylic acid inhibitor with PHD2
- PDB DOI: https://doi.org/10.2210/pdb8J1K/pdb
- Classification: OXIDOREDUCTASE/INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2023-04-13 Released: 2024-04-17
- Funding Organization(s): Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.308
- R-Value Work: 0.242
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Egl nine homolog 1 | 218 | Homo sapiens | Mutation(s): 0 Gene Names: EGLN1, C1orf12, PNAS-118, PNAS-137 EC: 1.14.11.29 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9GZT9 (Homo sapiens) Explore Q9GZT9 Go to UniProtKB: Q9GZT9 | |||||
PHAROS: Q9GZT9 GTEx: ENSG00000135766 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9GZT9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SY6 (Subject of Investigation/LOI) Query on SY6 | B [auth A] | N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide C20 H18 N6 O3 ROTOKWNRJPNVEV-CQSZACIVSA-N |  | ||
| MN Query on MN | C [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.308
- R-Value Work: 0.242
- Space Group: P 63
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.843 | α = 90 |
| b = 80.843 | β = 90 |
| c = 63.899 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-04-17 Deposition Author(s): Xu, J., Fu, Y., Ding, X., Meng, Q., Wang, L., Zhang, M., Ding, X., Ren, F., Zhavoronkov, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-04-17
Type: Initial release
