4F6S

Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-kinetic relationship study of CDK8/CycC specific compounds.

Schneider, E.V.Bottcher, J.Huber, R.Maskos, K.Neumann, L.

(2013) Proc.Natl.Acad.Sci.USA 110: 8081-8086

  • DOI: 10.1073/pnas.1305378110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In contrast with the very well explored concept of structure-activity relationship, similar studies are missing for the dependency between binding kinetics and compound structure of a protein ligand complex, the structure-kinetic relationship. Here, ...

    In contrast with the very well explored concept of structure-activity relationship, similar studies are missing for the dependency between binding kinetics and compound structure of a protein ligand complex, the structure-kinetic relationship. Here, we present a structure-kinetic relationship study of the cyclin-dependent kinase 8 (CDK8)/cyclin C (CycC) complex. The scaffold moiety of the compounds is anchored in the kinase deep pocket and extended with diverse functional groups toward the hinge region and the front pocket. These variations can cause the compounds to change from fast to slow binding kinetics, resulting in an improved residence time. The flip of the DFG motif ("DMG" in CDK8) to the inactive DFG-out conformation appears to have relatively little influence on the velocity of binding. Hydrogen bonding with the kinase hinge region contributes to the residence time but has less impact than hydrophobic complementarities within the kinase front pocket.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany. schneider@proteros.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 8
A
405Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.22, 2.7.11.23
Find proteins for P49336 (Homo sapiens)
Go to Gene View: CDK8
Go to UniProtKB:  P49336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-C
B
287Homo sapiensMutation(s): 0 
Gene Names: CCNC
Find proteins for P24863 (Homo sapiens)
Go to Gene View: CCNC
Go to UniProtKB:  P24863
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
0SQ
Query on 0SQ

Download SDF File 
Download CCD File 
A
1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea
C15 H20 N4 O
PXDGOKVFTJDAPC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.036α = 90.00
b = 71.395β = 90.00
c = 171.719γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references