5HVY | pdb_00005hvy

CDK8/CYCC IN COMPLEX WITH COMPOUND 20

PDB DOI: https://doi.org/10.2210/pdb5HVY/pdb

Classification: Transferase/Transcription
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-28 Released: 2016-04-20
Deposition Author(s): Kiefer, J.R., Schneider, E.V., Maskos, K., Bergeron, P., Koehler, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.220 (Depositor), 0.229 (DCC)
R-Value Work:
0.180 (Depositor), 0.188 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design and Development of a Series of Potent and Selective Type II Inhibitors of CDK8.

Bergeron, P., Koehler, M.F., Blackwood, E.M., Bowman, K., Clark, K., Firestein, R., Kiefer, J.R., Maskos, K., McCleland, M.L., Orren, L., Ramaswamy, S., Salphati, L., Schmidt, S., Schneider, E.V., Wu, J., Beresini, M.

(2016) ACS Med Chem Lett 7: 595-600

PubMed: 27326333 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6b00044
Primary Citation Related Structures:
5HVY

PubMed Abstract:
Using Sorafenib as a starting point, a series of potent and selective inhibitors of CDK8 was developed. When cocrystallized with CDK8 and cyclin C, these compounds exhibit a Type-II (DMG-out) binding mode.

Organizational Affiliation

Department of Discovery Chemistry, Department of Translational Oncology, Department of Structural Biology, Department of Small Molecule Biochemical Pharmacology, Department of Pathology, Department of Drug Metabolism, and Department of Protein Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content

Total Structure Weight: 81.41 kDa
Atom Count: 5,067
Modeled Residue Count: 602
Deposited Residue Count: 693
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	406	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	287	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
66X Query on 66X 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]	N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea C₂₂ H₂₈ F₃ N₇ O₂ LVIYMOOJJGCMCP-KRWDZBQOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT 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]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
66X	BindingDB: 5HVY	IC50: min: 17, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.220 (Depositor), 0.229 (DCC)
R-Value Work: 0.180 (Depositor), 0.188 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.184	α = 90
b = 71.859	β = 90
c = 180.821	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-04-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-20
Type: Initial release
Version 1.1: 2016-07-06
Changes: Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations