Download MendeleyNew thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer
Pernot, L., Novakovic, I., Perozzo, R., Raic-Malic, S., Scapozza, L.To be published.
4IVP | pdb_00004ivp
Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN51/20
- PDB DOI: https://doi.org/10.2210/pdb4IVP/pdb
- Classification: TRANSFERASE
- Organism(s): Human alphaherpesvirus 1 strain 17
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2013-01-23 Released: 2013-02-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.214 (Depositor), 0.210 (DCC)
- R-Value Work: 0.178 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.180 (Depositor)
Starting Model: experimental
View more details
This is version 1.2 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 |
| Thymidine kinase | 331 | Human alphaherpesvirus 1 strain 17 | Mutation(s): 0 Gene Names: TK, TK (UL23), UL23 EC: 2.7.1.21 |  | |
UniProt | |||||
Find proteins for P0DTH5 (Human herpesvirus 1 (strain 17)) Explore P0DTH5 Go to UniProtKB: P0DTH5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTH5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| I51 Query on I51 | C [auth A], F [auth B] | 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-5-methylpyrimidine-2,4(1H,3H)-dione C9 H12 N2 O4 IYYCMOUEXPXAQM-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | D [auth A], E [auth A], G [auth B], H [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.214 (Depositor), 0.210 (DCC)
- R-Value Work: 0.178 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.180 (Depositor)
Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.001 | α = 90 |
| b = 117.827 | β = 90 |
| c = 108.3 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| PHENIX | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2013-02-06 Deposition Author(s): Pernot, L., Novakovic, I., Westermaier, Y., Perozzo, R., Raic-Malic, S., Scapozza, L.
Revision History (Full details and data files)
- Version 1.0: 2013-02-06
Type: Initial release - Version 1.1: 2013-10-02
Changes: Experimental preparation, Structure summary - Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
