5XQX

Human CDK8-CYCC in complex with compound 4: N-methyl-4-(4-pyridyl)-1H-pyrrole-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb5XQX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2017-06-07 Released: 2017-08-09 
• Deposition Author(s): Zhou, Z., Xu, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Discovery of potent and selective CDK8 inhibitors through FBDD approach

Han, X., Jiang, M., Zhou, C., Zhou, Z., Xu, Z., Wang, L., Mayweg, A.V., Niu, R., Jin, T.G., Yang, S.

(2017) Bioorg Med Chem Lett 27: 4488-4492

• PubMed: 28802632 
• DOI: https://doi.org/10.1016/j.bmcl.2017.07.080
• Primary Citation of Related Structures:  
  5XQX, 5XS2


• PubMed Abstract: 
  

  A fragment library screen was carried out to identify starting points for novel CDK8 inhibitors. Optimization of a fragment hit guided by co-crystal structures led to identification of a novel series of potent CDK8 inhibitors which are highly ligand efficient, kinase selective and cellular active. Compound 16 was progressed to a mouse pharmacokinetic study and showed good oral bioavailability.

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Organizational Affiliation: 

Medicinal Chemistry, Roche Innovation Center Shanghai, Bldg 5, 720 Cailun Road, Shanghai 201203, China. Electronic address: [e-mail].

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: 75.87 kDa 
• Atom Count: 5,214 
• Modelled Residue Count: 603 
• Deposited Residue Count: 643 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 8	A	380	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	263	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8CC (Subject of Investigation/LOI)	D [auth A]	N-methyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide C11 H11 N3 O CUQAMHMOOUOTLK-UHFFFAOYSA-N
GOL	C [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8CC	BindingDB:  5XQX	IC50: 410 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.973	α = 90
b = 73.966	β = 90
c = 168.483	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Zhou, Z., Xu, Z.H.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Database references
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references