6H51

Crystal structure of human KDM5B in complex with compound 34f

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays.

Le Bihan, Y.V., Lanigan, R.M., Atrash, B., McLaughlin, M.G., Velupillai, S., Malcolm, A.G., England, K.S., Ruda, G.F., Mok, N.Y., Tumber, A., Tomlin, K., Saville, H., Shehu, E., McAndrew, C., Carmichael, L., Bennett, J.M., Jeganathan, F., Eve, P., Donovan, A., Hayes, A., Wood, F., Raynaud, F.I., Fedorov, O., Brennan, P.E., Burke, R., van Montfort, R.L.M., Rossanese, O.W., Blagg, J., Bavetsias, V.

(2019) Eur.J.Med.Chem. 177: 316-337

  • DOI: 10.1016/j.ejmech.2019.05.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences bet ...

    Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.

    Organizational Affiliation: 

    Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK. Electronic address: julian.blagg@icr.ac.uk.,Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.,Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK. Electronic address: vassilios.bavetsias@icr.ac.uk.,Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
A
481Homo sapiensMutation(s): 0 
Gene Names: KDM5B (JARID1B, PLU1, RBBP2H1)
EC: 1.14.11.-
Find proteins for Q9UGL1 (Homo sapiens)
Go to Gene View: KDM5B
Go to UniProtKB:  Q9UGL1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4
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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN
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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS
Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
FQK
Query on FQK
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Download CCD File 
A
8-[4-[1-(cyclobutylmethyl)piperidin-4-yl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
C20 H24 N6 O
FQYVJQRHNLIPIK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.182 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 142.000α = 90.00
b = 142.000β = 90.00
c = 152.410γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release