4C13 | pdb_00004c13

x-ray crystal structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4C13

Ligand Structure Quality Assessment 


This is version 2.4 of the entry. See complete history

Literature

Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy.

Wang, L.Shao, X.Zhong, T.Wu, Y.Xu, A.Sun, X.Gao, H.Liu, Y.Lan, T.Tong, Y.Tao, X.Du, W.Wang, W.Chen, Y.Li, T.Meng, X.Deng, H.Yang, B.He, Q.Ying, M.Rao, Y.

(2021) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-021-00742-5
  • Primary Citation Related Structures: 
    4C13

  • PubMed Abstract: 

    The discovery of effective therapeutic treatments for cancer via cell differentiation instead of antiproliferation remains a great challenge. Cyclin-dependent kinase 2 (CDK2) inactivation, which overcomes the differentiation arrest of acute myeloid leukemia (AML) cells, may be a promising method for AML treatment. However, there is no available selective CDK2 inhibitor. More importantly, the inhibition of only the enzymatic function of CDK2 would be insufficient to promote notable AML differentiation. To further validate the role and druggability of CDK2 involved in AML differentiation, a suitable chemical tool is needed. Therefore, we developed first-in-class CDK2-targeted proteolysis-targeting chimeras (PROTACs), which promoted rapid and potent CDK2 degradation in different cell lines without comparable degradation of other targets, and induced remarkable differentiation of AML cell lines and primary patient cells. These data clearly demonstrated the practicality and importance of PROTACs as alternative tools for verifying CDK2 protein functions.


  • Organizational Affiliation
    • MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 56.51 kDa 
  • Atom Count: 4,075 
  • Modeled Residue Count: 490 
  • Deposited Residue Count: 501 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE501Staphylococcus aureusMutation(s): 0 
EC: 6.3.2.7
UniProt
Find proteins for Q2FZP6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZP6 
Go to UniProtKB:  Q2FZP6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FZP6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UML

Query on UML



Download:Ideal Coordinates CCD File
E [auth A]Uridine 5'Diphospho N-acetyl muramoyl-L-Alanyl-D-Glutamyl-L-Lysine
C34 H55 N7 O24 P2
WXBLSQNZKMJACT-BYEZXYKXSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K

Query on K



Download:Ideal Coordinates CCD File
G [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.82α = 90
b = 54.03β = 92.02
c = 70.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2013-11-27
    Changes: Database references
  • Version 2.0: 2017-06-28
    Changes: Advisory, Atomic model, Data collection
  • Version 2.1: 2017-09-13
    Changes: Data collection
  • Version 2.2: 2018-06-20
    Changes: Data collection, Structure summary
  • Version 2.3: 2021-03-17
    Changes: Database references, Derived calculations, Other
  • Version 2.4: 2025-04-09
    Changes: Data collection, Database references, Structure summary