5HVY

CDK8/CYCC IN COMPLEX WITH COMPOUND 20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design and Development of a Series of Potent and Selective Type II Inhibitors of CDK8.

Bergeron, P.Koehler, M.F.Blackwood, E.M.Bowman, K.Clark, K.Firestein, R.Kiefer, J.R.Maskos, K.McCleland, M.L.Orren, L.Ramaswamy, S.Salphati, L.Schmidt, S.Schneider, E.V.Wu, J.Beresini, M.

(2016) ACS Med Chem Lett 7: 595-600

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00044
  • Primary Citation of Related Structures:  
    5HVY

  • PubMed Abstract: 

    Using Sorafenib as a starting point, a series of potent and selective inhibitors of CDK8 was developed. When cocrystallized with CDK8 and cyclin C, these compounds exhibit a Type-II (DMG-out) binding mode.


  • Organizational Affiliation

    Department of Discovery Chemistry, Department of Translational Oncology, Department of Structural Biology, Department of Small Molecule Biochemical Pharmacology, Department of Pathology, Department of Drug Metabolism, and Department of Protein Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 8406Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49336 (Homo sapiens)
Explore P49336 
Go to UniProtKB:  P49336
PHAROS:  P49336
GTEx:  ENSG00000132964 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49336
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-C287Homo sapiensMutation(s): 0 
Gene Names: CCNC
UniProt & NIH Common Fund Data Resources
Find proteins for P24863 (Homo sapiens)
Explore P24863 
Go to UniProtKB:  P24863
PHAROS:  P24863
GTEx:  ENSG00000112237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24863
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
66X
Query on 66X

Download Ideal Coordinates CCD File 
C [auth A]N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea
C22 H28 F3 N7 O2
LVIYMOOJJGCMCP-KRWDZBQOSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
66X Binding MOAD:  5HVY IC50: 17.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.184α = 90
b = 71.859β = 90
c = 180.821γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references