8VF6

Crystal structure of Serine/threonine-protein kinase 33 (STK33) Kinase Domain in complex with inhibitor CDD-2211


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Reversible male contraception by targeted inhibition of serine/threonine kinase 33.

Ku, A.F.Sharma, K.L.Ta, H.M.Sutton, C.M.Bohren, K.M.Wang, Y.Chamakuri, S.Chen, R.Hakenjos, J.M.Jimmidi, R.Kent, K.Li, F.Li, J.Y.Ma, L.Madasu, C.Palaniappan, M.Palmer, S.S.Qin, X.Robers, M.B.Sankaran, B.Tan, Z.Vasquez, Y.M.Wang, J.Wilkinson, J.Yu, Z.Ye, Q.Young, D.W.Teng, M.Kim, C.Matzuk, M.M.

(2024) Science 384: 885-890

  • DOI: https://doi.org/10.1126/science.adl2688
  • Primary Citation of Related Structures:  
    8VF6

  • PubMed Abstract: 

    Men or mice with homozygous serine/threonine kinase 33 ( STK33 ) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.


  • Organizational Affiliation

    Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 33
A, B
286Homo sapiensMutation(s): 0 
Gene Names: STK33
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYT3 (Homo sapiens)
Explore Q9BYT3 
Go to UniProtKB:  Q9BYT3
PHAROS:  Q9BYT3
GTEx:  ENSG00000130413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYT3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AAY (Subject of Investigation/LOI)
Query on A1AAY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
{3-[([1,1'-biphenyl]-2-yl)ethynyl]-1H-indazol-5-yl}[(3R)-3-(dimethylamino)pyrrolidin-1-yl]methanone
C28 H26 N4 O
ZRBBUAGMFWALNG-HSZRJFAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.21α = 90
b = 87.92β = 90
c = 98.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesNV- 001902

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release