4F9C

Human CDC7 kinase in complex with DBF4 and XL413


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human CDC7 kinase in complex with its activator DBF4.

Hughes, S.Elustondo, F.Di Fonzo, A.Leroux, F.G.Wong, A.C.Snijders, A.P.Matthews, S.J.Cherepanov, P.

(2012) Nat.Struct.Mol.Biol. 19: 1101-1107

  • DOI: 10.1038/nsmb.2404
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CDC7 is a serine/threonine kinase that is essential for the initiation of eukaryotic DNA replication. CDC7 activity is controlled by its activator, DBF4. Here we present crystal structures of human CDC7-DBF4 in complex with a nucleotide or ATP-compet ...

    CDC7 is a serine/threonine kinase that is essential for the initiation of eukaryotic DNA replication. CDC7 activity is controlled by its activator, DBF4. Here we present crystal structures of human CDC7-DBF4 in complex with a nucleotide or ATP-competing small molecules, revealing the active and inhibited forms of the kinase, respectively. DBF4 wraps around CDC7, burying approximately 6,000 Å(2) of hydrophobic molecular surface in a bipartite interface. The effector domain of DBF4, containing conserved motif C, is essential and sufficient to support CDC7 kinase activity by binding to the kinase N-terminal lobe and stabilizing its canonical αC helix. DBF4 motif M latches onto the C-terminal lobe of the kinase, acting as a tethering domain. Our results elucidate the structural basis for binding to and activation of CDC7 by DBF4 and provide a framework for the design of more potent and specific CDC7 inhibitors.


    Organizational Affiliation

    Cancer Research UK, London Research Institute, Clare Hall Laboratories, Potters Bar, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle 7-related protein kinase
A
361Homo sapiensGene Names: CDC7 (CDC7L1)
EC: 2.7.11.1
Find proteins for O00311 (Homo sapiens)
Go to Gene View: CDC7
Go to UniProtKB:  O00311
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein DBF4 homolog A
B
144Homo sapiensGene Names: DBF4 (ASK, DBF4A, ZDBF1)
Find proteins for Q9UBU7 (Homo sapiens)
Go to Gene View: DBF4
Go to UniProtKB:  Q9UBU7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
0SX
Query on 0SX

Download SDF File 
Download CCD File 
A
8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one
C14 H12 Cl N3 O2
JJWLXRKVUJDJKG-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0SXIC50: 3.4 - 140 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.270α = 90.00
b = 61.270β = 90.00
c = 238.940γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Data collection, Source and taxonomy
  • Version 1.3: 2017-11-15
    Type: Refinement description