6CSW | pdb_00006csw

Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor

PDB DOI: https://doi.org/10.2210/pdb6CSW/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-03-21 Released: 2018-04-04
Deposition Author(s): dos Reis, C.V., de Souza, G.P., Counago, R.M., Chiodi, C.G., Azevedo, A., Guimaraes, C., Mascarello, A., Gama, F., Ferreira, M., Massirer, K.B., Arruda, P., Edwards, A.M., Elkins, J.M., Structural Genomics Consortium (SGC)
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor

dos Reis, C.V., de Souza, G.P., Counago, R.M., Azevedo, H., Guimaraes, C., Mascarello, A., Gama, F., Ferreira, M., Massirer, K.B., Arruda, P., Edwards, A.M., Elkins, J.M., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 168.61 kDa
Atom Count: 10,829
Modeled Residue Count: 1,255
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBY Query on FBY Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain Z [auth D] MOL2 format, chain J [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain J [auth B] mmCIF format, chain Z [auth D]	J [auth B], Z [auth D]	(7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-7,8-dihydropteridin-6(5H)-one C₁₈ H₂₁ F₂ N₅ O₂ IQHUYDHFNRXPGH-SNVBAGLBSA-N		Interactions Focus chain J [auth B] Focus chain Z [auth D] Interactions & Density Focus chain J [auth B] Focus chain Z [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] E [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], K [auth B], L [auth B], M [auth B], R [auth C], S [auth C], T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain IA [auth D] SDF format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain GA [auth D]	GA [auth D] HA [auth D] IA [auth D] JA [auth D] KA [auth D] GA [auth D], HA [auth D], IA [auth D], JA [auth D], KA [auth D], LA [auth D], MA [auth D], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain NA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain NA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain NA [auth D]	G [auth A], NA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain NA [auth D] Interactions & Density Focus chain G [auth A] Focus chain NA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain Y [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain Y [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain Y [auth C]	OA [auth D], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain OA [auth D] Focus chain Y [auth C] Interactions & Density Focus chain OA [auth D] Focus chain Y [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
FBY	BindingDB: 6CSW	Ki: 128 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.233 (Depositor), 0.237 (DCC)
R-Value Work: 0.188 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.83	α = 90
b = 96.987	β = 90
c = 191.67	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-04-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History (Full details and data files)

Version 1.0: 2018-04-04
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2020-12-16
Changes: Other, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description