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 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report



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:  
    6H4Z, 6H4S, 6H4R, 6H4U, 6H4T, 6H4W, 6H4V, 6H4Y, 6H4X, 6H4O

  • 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 between ...

    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: 

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK. Electronic address: vassilios.bavetsias@icr.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B A481Homo sapiensMutation(s): 0 
Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for Q9UGL1 (Homo sapiens)
Explore Q9UGL1 
Go to UniProtKB:  Q9UGL1
NIH Common Fund Data Resources
PHAROS:  Q9UGL1
GTEx:  ENSG00000117139
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FQK
Query on FQK
Download Ideal Coordinates 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
PO4
Query on PO4
Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FQKKi:  16   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142α = 90
b = 142β = 90
c = 152.41γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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