5V84 | pdb_00005v84

CECR2 in complex with Cpd6 (6-allyl-N,2-dimethyl-7-oxo-N-(1-(1-phenylethyl)piperidin-4-yl)-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-4-carboxamide)

PDB DOI: https://doi.org/10.2210/pdb5V84/pdb

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

Deposited: 2017-03-21 Released: 2017-06-14
Deposition Author(s): Murray, J.M., Kiefer, J.R., Jayaran, H., Bellon, S., Boy, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.222 (Depositor), 0.237 (DCC)
R-Value Work:
0.206 (Depositor), 0.214 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

GNE-886: A Potent and Selective Inhibitor of the Cat Eye Syndrome Chromosome Region Candidate 2 Bromodomain (CECR2).

Crawford, T.D., Audia, J.E., Bellon, S., Burdick, D.J., Bommi-Reddy, A., Cote, A., Cummings, R.T., Duplessis, M., Flynn, E.M., Hewitt, M., Huang, H.R., Jayaram, H., Jiang, Y., Joshi, S., Kiefer, J.R., Murray, J., Nasveschuk, C.G., Neiss, A., Pardo, E., Romero, F.A., Sandy, P., Sims, R.J., Tang, Y., Taylor, A.M., Tsui, V., Wang, J., Wang, S., Wang, Y., Xu, Z., Zawadzke, L., Zhu, X., Albrecht, B.K., Magnuson, S.R., Cochran, A.G.

(2017) ACS Med Chem Lett 8: 737-741

PubMed: 28740608 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.7b00132
Primary Citation Related Structures:
5V84

PubMed Abstract:
The biological function of bromodomains, epigenetic readers of acetylated lysine residues, remains largely unknown. Herein we report our efforts to discover a potent and selective inhibitor of the bromodomain of cat eye syndrome chromosome region candidate 2 (CECR2). Screening of our internal medicinal chemistry collection led to the identification of a pyrrolopyridone chemical lead, and subsequent structure-based drug design led to a potent and selective CECR2 bromodomain inhibitor (GNE-886) suitable for use as an in vitro tool compound.

Organizational Affiliation

Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content

Total Structure Weight: 68.48 kDa
Atom Count: 3,517
Modeled Residue Count: 406
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cat eye syndrome critical region protein 2	A, B, C, D	140	Homo sapiens	Mutation(s): 0 Gene Names: CECR2, KIAA1740
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXF3 (Homo sapiens) Explore Q9BXF3 Go to UniProtKB: Q9BXF3
PHAROS: Q9BXF3 GTEx: ENSG00000099954
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BXF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
96V Query on 96V Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain J [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D]	F [auth A], G [auth B], H [auth C], J [auth D]	N,2-dimethyl-7-oxo-N-{1-[(1S)-1-phenylethyl]piperidin-4-yl}-6-(prop-2-en-1-yl)-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-4- carboxamide C₂₆ H₃₂ N₄ O₂ WFCPQMAYBTUYAR-IBGZPJMESA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth D]	E [auth A], I [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
96V	BindingDB: 5V84	IC50: 190 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.222 (Depositor), 0.237 (DCC)
R-Value Work: 0.206 (Depositor), 0.214 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.184	α = 90
b = 116.488	β = 90
c = 132.93	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-06-14
Type: Initial release
Version 1.1: 2017-08-09
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary