5VD4 | pdb_00005vd4

CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-016, a MK1775 analougue

• PDB DOI: https://doi.org/10.2210/pdb5VD4/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-01 Released: 2018-04-04 
• Deposition Author(s): Zhu, J.-Y., Schonbrunn, E.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Structural basis of Wee family kinase inhibition by small molecules

Zhu, J.-Y., Schonbrunn, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.39 kDa 
• Atom Count: 2,187 
• Modeled Residue Count: 261 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Wee1-like protein kinase	A	289	Homo sapiens	Mutation(s): 0  Gene Names: WEE1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P30291 (Homo sapiens) Explore P30291  Go to UniProtKB:  P30291
PHAROS:  P30291 GTEx:  ENSG00000166483

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
99J	B [auth A]	6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1-{6-[(1S)-2,2,2-trifluoro-1-hydroxyethyl]pyridin-2-yl}-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one C26 H27 F3 N8 O2 DQUHCAHRQQRKGR-QFIPXVFZSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.31	α = 90
b = 43.78	β = 103.04
c = 64.86	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Zhu, J.-Y., Schonbrunn, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	UO1 HD076542

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description