8WJY

PKMYT1_Cocrystal_Cpd 4

• PDB DOI: https://doi.org/10.2210/pdb8WJY/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2023-09-26 Released: 2023-11-22 
• Deposition Author(s): Wang, Y., Wang, C., Liu, T., Qi, H., Chen, S., Cai, X., Zhang, M., Aliper, A., Ren, F., Ding, X., Zhavoronkov, A.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.217 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

PKMYT1_Cocrystal_Cpd 4

Wang, Y., Wang, C., Liu, T., Qi, H., Chen, S., Cai, X., Zhang, M., Aliper, A., Ren, F., Ding, X., Zhavoronkov, A.

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: fluorescence resonance energy transfer

Macromolecule Content

• Total Structure Weight: 35.1 kDa 
• Atom Count: 2,625 
• Modelled Residue Count: 291 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase	A	311	Homo sapiens	Mutation(s): 0  Gene Names: PKMYT1, MYT1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99640 (Homo sapiens) Explore Q99640  Go to UniProtKB:  Q99640
PHAROS:  Q99640 GTEx:  ENSG00000127564

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W9X (Subject of Investigation/LOI)	B [auth A]	[6-azanyl-5-(2,6-dimethyl-3-oxidanyl-phenyl)-2,3-dimethyl-pyrrolo[2,3-b]pyrazin-7-yl]-(6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazin-5-yl)methanone C23 H25 N7 O2 BGGQMRVFAYRPSL-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.217 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.01	α = 90
b = 55.81	β = 90
c = 113.92	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Wang, Y., Wang, C., Liu, T., Qi, H., Chen, S., Cai, X., Zhang, M., Aliper, A., Ren, F., Ding, X., Zhavoronkov, A.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release