5HVY

CDK8/CYCC IN COMPLEX WITH COMPOUND 20

• PDB DOI: https://doi.org/10.2210/pdb5HVY/pdb

• Classification: Transferase/Transcription
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-28 Released: 2016-04-20 
• Deposition Author(s): Kiefer, J.R., Schneider, E.V., Maskos, K., Bergeron, P., Koehler, M.

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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 

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

• PubMed: 27326333 
• 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.41 kDa 
• Atom Count: 5,067 
• Modelled Residue Count: 602 
• Deposited Residue Count: 693 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 8	A	406	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-C	B	287	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
66X	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	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding 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 = 72.184	α = 90
b = 71.859	β = 90
c = 180.821	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Kiefer, J.R., Schneider, E.V., Maskos, K., Bergeron, P., Koehler, M.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations