6VXU | pdb_00006vxu

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
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(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 (Depositor), 0.210 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471

Guimaraes, C.R., Counago, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 167.59 kDa
Atom Count: 10,525
Modeled Residue Count: 1,251
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase VRK1	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99986
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RTJ (Subject of Investigation/LOI) Query on RTJ Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain Q [auth D]
VBD (Subject of Investigation/LOI) Query on VBD Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	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		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C], R [auth D], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
RTJ	BindingDB: 6VXU	Ki: 23 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203 (Depositor), 0.210 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.185 (Depositor)

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 Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

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