Download MendeleyStructure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471
Guimaraes, C.R., Counago, R.M.To be published.
6VXU
Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471
- PDB DOI: https://doi.org/10.2210/pdb6VXU/pdb
- Classification: TRANSFERASE/TRANSFERASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2020-02-24 Released: 2021-03-03
- Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.203
- R-Value Work: 0.184
- R-Value Observed: 0.185
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
Currently 6VXU does not have a validation slider image.
This is version 1.1 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 |
| Serine/threonine-protein kinase VRK1 | 364 | Homo sapiens | Mutation(s): 11 Gene Names: VRK1 EC: 2.7.11.1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q99986 (Homo sapiens) Explore Q99986 Go to UniProtKB: Q99986 | |||||
PHAROS: Q99986 GTEx: ENSG00000100749 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q99986 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| VBD (Subject of Investigation/LOI) Query on VBD | L [auth C] | (7S)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one C20 H19 F2 N5 O2 VCABIQKTZQAYKL-NSHDSACASA-N |  | ||
| RTJ (Subject of Investigation/LOI) Query on RTJ | E [auth A], H [auth B], Q [auth D] | (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one C20 H19 F2 N5 O2 VCABIQKTZQAYKL-LLVKDONJSA-N |  | ||
| SO4 Query on SO4 | F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | P [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.203
- R-Value Work: 0.184
- R-Value Observed: 0.185
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 91.771 | α = 90 |
| b = 96.3 | β = 90 |
| c = 191.988 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
Structure Validation
Currently 6VXU does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2021-03-03 Deposition Author(s): dos Reis, C.V., Dutra, L.A., Gama, F.H., Mascarello, A., Azevedo, H., Guimaraes, C.R., Massirer, K.B., Arruda, P., Edwards, A.M., Counago, R.M., Structural Genomics Consortium (SGC)
| Funding Organization | Location | Grant Number |
|---|---|---|
| Sao Paulo Research Foundation (FAPESP) | Brazil | 2013/50724-5 |
| Brazilian National Council for Scientific and Technological Development (CNPq) | Brazil | 465651/2014-3 |
| Sao Paulo Research Foundation (FAPESP) | Brazil | 2014/50897-0 |
Revision History (Full details and data files)
- Version 1.0: 2021-03-03
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
