5FGK | pdb_00005fgk

CDK8-CYCC IN COMPLEX WITH 8-[3-(3-Amino-1H-indazol-6-yl)-5-chloro- pyridine-4-yl]-2,8-diaza-spiro[4.5]decan-1-one

PDB DOI: https://doi.org/10.2210/pdb5FGK/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-12-20 Released: 2016-02-03
Deposition Author(s): Musil, D., Blagg, J., Mallinger, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.237 (Depositor), 0.244 (DCC)
R-Value Work:
0.221 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19.

Mallinger, A., Schiemann, K., Rink, C., Stieber, F., Calderini, M., Crumpler, S., Stubbs, M., Adeniji-Popoola, O., Poeschke, O., Busch, M., Czodrowski, P., Musil, D., Schwarz, D., Ortiz-Ruiz, M.J., Schneider, R., Thai, C., Valenti, M., de Haven Brandon, A., Burke, R., Workman, P., Dale, T., Wienke, D., Clarke, P.A., Esdar, C., Raynaud, F.I., Eccles, S.A., Rohdich, F., Blagg, J.

(2016) J Med Chem 59: 1078-1101

PubMed: 26796641 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.5b01685
Primary Citation Related Structures:
5FGK, 5HBE, 5HBH, 5HBJ

PubMed Abstract:
The Mediator complex-associated cyclin-dependent kinase CDK8 has been implicated in human disease, particularly in colorectal cancer where it has been reported as a putative oncogene. Here we report the discovery of 109 (CCT251921), a potent, selective, and orally bioavailable inhibitor of CDK8 with equipotent affinity for CDK19. We describe a structure-based design approach leading to the discovery of a 3,4,5-trisubstituted-2-aminopyridine series and present the application of physicochemical property analyses to successfully reduce in vivo metabolic clearance, minimize transporter-mediated biliary elimination while maintaining acceptable aqueous solubility. Compound 109 affords the optimal compromise of in vitro biochemical, pharmacokinetic, and physicochemical properties and is suitable for progression to animal models of cancer.

Organizational Affiliation

Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K.

Macromolecule Content

Total Structure Weight: 75.01 kDa
Atom Count: 5,225
Modeled Residue Count: 597
Deposited Residue Count: 630
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 8	A	364	Homo sapiens	Mutation(s): 0 Gene Names: CDK8 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49336 (Homo sapiens) Explore P49336 Go to UniProtKB: P49336
PHAROS: P49336 GTEx: ENSG00000132964
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49336
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-C	B	266	Homo sapiens	Mutation(s): 0 Gene Names: CCNC
UniProt & NIH Common Fund Data Resources
Find proteins for P24863 (Homo sapiens) Explore P24863 Go to UniProtKB: P24863
PHAROS: P24863 GTEx: ENSG00000112237
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24863
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5XG Query on 5XG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one C₂₀ H₂₁ Cl N₆ O ZVSGCPGPQNLKLU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth A] mmCIF format, chain E [auth A]	E [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth A] Interactions & Density Focus chain E [auth A] Focus chain L [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B]