Download MendeleyHalogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases
Jiang, L.G., Zhang, X., Zhou, Y., Chen, Y.Y., Luo, Z.P., Li, J.Y., Yuan, C., Huang, M.D.(2018) RSC Adv 8: 28189-28197
5YC7
The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH7.4
- PDB DOI: https://doi.org/10.2210/pdb5YC7/pdb
- Entry: 5YC7 supersedes: 4JNL
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Komagataella pastoris
- Mutation(s): No
- Deposited: 2017-09-06 Released: 2018-10-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.262
- R-Value Work: 0.212
- R-Value Observed: 0.214
Starting Model: experimental
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This is version 1.2 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 |
| Urokinase-type plasminogen activator | A [auth U] | 246 | Homo sapiens | Mutation(s): 0 Gene Names: PLAU EC: 3.4.21.73 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00749 (Homo sapiens) Explore P00749 Go to UniProtKB: P00749 | |||||
PHAROS: P00749 GTEx: ENSG00000122861 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00749 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PZH Query on PZH | B [auth U] | 1-(4-BROMOPHENYL)METHANAMINE C7 H8 Br N XRNVSPDQTPVECU-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | C [auth U] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.262
- R-Value Work: 0.212
- R-Value Observed: 0.214
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 121.575 | α = 90 |
| b = 121.575 | β = 90 |
| c = 42.212 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data processing |
Entry History
Deposition Data
- Released Date: 2018-10-03 Deposition Author(s): Jiang, L.G., Zhang, X., Huang, M.D.
- This entry supersedes: 4JNL
Revision History (Full details and data files)
- Version 1.0: 2018-10-03
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description - Version 1.2: 2024-10-30
Changes: Structure summary
