ISDA

Deposition Date 2017-09-25

Release Date 2017-12-27

Last Version Date 2024-11-20

Entry Detail

PDB ID:

6B3W

Keywords:

METAL BINDING PROTEIN

Title:

Structure of Hs/AcPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one

Biological Source:

Source Organism:

Anolis carolinensis (Taxon ID: 28377)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.05 Å

R-Value Free:

0.28

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Enhancer of zeste 2 polycomb repressive complex 2 subunit,Enhancer of zeste 2 polycomb repressive complex 2 subunit
Gene (Uniprot):EZH2
Chain IDs:A, B
Chain Length:643
Number of Molecules:2
Biological Source:Anolis carolinensis

UniProt ID:G1KPH4 Pfam ID:PF11616, PF18118, PF21358, PF18264, PF00856

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Polycomb protein EED
Gene (Uniprot):EED
Chain IDs:C (auth: E), D (auth: F)
Chain Length:362
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:O75530 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Polycomb protein SUZ12
Gene (Uniprot):SUZ12
Chain IDs:E (auth: S), F (auth: T)
Chain Length:191
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q15022 Pfam ID:PF09733

Ligand Molecules

CJG

Primary Citation

Optimization of Orally Bioavailable Enhancer of Zeste Homolog 2 (EZH2) Inhibitors Using Ligand and Property-Based Design Strategies: Identification of Development Candidate (R)-5,8-Dichloro-7-(methoxy(oxetan-3-yl)methyl)-2-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-3,4-dihydroisoquinolin-1(2H)-one (PF-06821497).

Kung, P.P, Bingham, P, Brooun, A, Collins, M, Deng, Y.L, Dinh, D, Fan, C, Gajiwala, K.S, Grantner, R, Gukasyan, H.J, Hu, W, Huang, B, Kania, R, Kephart, S.E, Krivacic, C, Kumpf, R.A, Khamphavong, P, Kraus, M, Liu, W, Maegley, K.A, Nguyen, L, Ren, S, Richter, D, Rollins, R.A, Sach, N, Sharma, S, Sherrill, J, Spangler, J, Stewart, A.E, Sutton, S, Uryu, S, Verhelle, D, Wang, H, Wang, S, Wythes, M, Xin, S, Yamazaki, S, Zhu, H, Zhu, J, Zehnder, L, Edwards, M.Show

J. Med. Chem. 61 650 665 (2018)

PMID: 29211475 DOI: 10.1021/acs.jmedchem.7b01375

Abstact

A new series of lactam-derived EZH2 inhibitors was designed via ligand-based and physicochemical-property-based strategies to address metabolic stability and thermodynamic solubility issues associated with previous lead compound 1. The new inhibitors incorporated an sp3 hybridized carbon atom at the 7-position of the lactam moiety present in lead compound 1 as a replacement for a dimethylisoxazole group. This transformation enabled optimization of the physicochemical properties and potency compared to compound 1. Analysis of relationships between calculated log D (clogD) values and in vitro metabolic stability and permeability parameters identified a clogD range that afforded an increased probability of achieving favorable ADME data in a single molecule. Compound 23a exhibited the best overlap of potency and pharmaceutical properties as well as robust tumor growth inhibition in vivo and was therefore advanced as a development candidate (PF-06821497). A crystal structure of 23a in complex with the three-protein PRC2 complex enabled understanding of the key structural features required for optimal binding.

Legend

Protein

Chemical

Disease

Primary Citation of related structures