7VDS

The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of Highly Selective Inhibitors of CDK5.

Daniels, M.H.Malojcic, G.Clugston, S.L.Williams, B.Coeffet-Le Gal, M.Pan-Zhou, X.R.Venkatachalan, S.Harmange, J.C.Ledeboer, M.

(2022) J Med Chem 65: 3575-3596

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02069
  • Primary Citation of Related Structures:  
    7VDP, 7VDQ, 7VDR, 7VDS, 7VDU

  • PubMed Abstract: 

    Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent monogenic human disease, but to date, only one therapy (tolvaptan) is approved to treat kidney cysts in ADPKD patients. Cyclin-dependent kinase 5 (CDK5), an atypical member of the cyclin-dependent kinase family, has been implicated as a target for treating ADPKD. However, no compounds have been disclosed to date that selectively inhibit CDK5 while sparing the broader CDK family members. Herein, we report the discovery of CDK5 inhibitors, including GFB-12811 , that are highly selective over the other tested kinases. In cellular assays, our compounds demonstrate CDK5 target engagement while avoiding anti-proliferative effects associated with inhibiting other CDKs. In addition, we show that the compounds in this series exhibit promising in vivo PK profiles, enabling their use as tool compounds for interrogating the role of CDK5 in ADPKD and other diseases.


  • Organizational Affiliation

    Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent-like kinase 5, p25
A, B
292Homo sapiensMutation(s): 0 
Gene Names: CDK5CDKN5
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q00535 (Homo sapiens)
Explore Q00535 
Go to UniProtKB:  Q00535
PHAROS:  Q00535
GTEx:  ENSG00000164885 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00535
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 5 activator 1
C, D
209Homo sapiensMutation(s): 0 
Gene Names: CDK5R1CDK5RNCK5A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15078 (Homo sapiens)
Explore Q15078 
Go to UniProtKB:  Q15078
PHAROS:  Q15078
GTEx:  ENSG00000176749 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15078
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
61U (Subject of Investigation/LOI)
Query on 61U

Download Ideal Coordinates CCD File 
E [auth A]5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile
C27 H31 F N6 O2
ODDUUXAHBDCKIJ-HHHXNRCGSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
IA [auth C]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
IA [auth C],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth B]
GA [auth B]
HA [auth B]
JA [auth C]
KA [auth C]
FA [auth B],
GA [auth B],
HA [auth B],
JA [auth C],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
Z [auth A],
ZA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.06α = 90
b = 118.06β = 90
c = 153.69γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description