PDB-5v84: CECR2 in complex with Cpd6 (6-allyl-N,2-dimethyl-7-oxo-N-(1-(1-ph...

ID or keywords:

Entry

Database: PDB / ID: 5v84

Title

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)

Components

Cat eye syndrome critical region protein 2

Keywords

Transcription/Inhibitor / Bromodomain / SBDD / Transcription-Inhibitor complex

Function / homology

Function and homology information

CERF complex / neural fold formation / inner ear receptor cell stereocilium organization / cytoskeleton-dependent cytokinesis / apoptotic DNA fragmentation / ATP-dependent chromatin remodeler activity / execution phase of apoptosis / cochlea development / single fertilization / vesicle-mediated transport ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.7 Å

Authors

Murray, J.M. / Kiefer, J.R. / Jayaran, H. / Bellon, S. / Boy, F.

Citation

Journal: ACS Med Chem Lett / Year: 2017
Title: GNE-886: A Potent and Selective Inhibitor of the Cat Eye Syndrome Chromosome Region Candidate 2 Bromodomain (CECR2).
Authors: 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. / ...

History

Deposition	Mar 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5v84.cif.gz	192.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5v84.ent.gz	154.3 KB	Display	PDB format
PDBx/mmJSON format	5v84.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5v84_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5v84_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5v84_validation.xml.gz	16.8 KB	Display
Data in CIF	5v84_validation.cif.gz	22.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v8/5v84 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/5v84	HTTPS FTP

-
Related structure data

Related structure data	3nxbS S: Starting model for refinement
Similar structure data	4g59-1 4g59-2 4by5-1 4nlo-d 1khv-2 4nox-d 4nru-2 5lzi-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cat eye syndrome critical region protein 2

B: Cat eye syndrome critical region protein 2

C: Cat eye syndrome critical region protein 2

D: Cat eye syndrome critical region protein 2

hetero molecules

68.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	101.184, 116.488, 132.930
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

#1: Protein	Cat eye syndrome critical region protein 2 Mass: 16639.842 Da / Num. of mol.: 4 / Fragment: UNP residues 404-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CECR2, KIAA1740 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXF3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-96V / 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 / 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 Mass: 432.558 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₆H₃₂N₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.2 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 1.5 M lithium sulfate, 0.1 M Tris-HCl pH 8.5

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.7→43.81 Å / Num. obs: 21604 / % possible obs: 99.9 % / Redundancy: 6.2 % / B_iso Wilson estimate: 72.81 Å² / R_merge(I) obs: 0.112 / Χ²: 1.036 / Net I/σ(I): 6.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Χ²	Diffraction-ID	% possible all
2.7-2.8	6.2	0.853	1.008	1	100
2.8-2.91	6.3	0.664	1.058	1	100
2.91-3.04	6.3	0.491	1.066	1	100
3.04-3.2	6.3	0.325	1.051	1	100
3.2-3.4	6.3	0.23	1.046	1	100
3.4-3.66	6.2	0.14	1.052	1	100
3.66-4.03	6.2	0.099	1.004	1	100
4.03-4.62	6.2	0.079	1.012	1	100
4.62-5.81	6.1	0.084	1.05	1	99.9
5.81-50	5.9	0.034	1.013	1	99.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
BUSTER	2.11.7	refinement
PDB_EXTRACT	3.22	data extraction
PHASER		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NXB

3nxb

Resolution: 2.7→43.81 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.93 / R_factor R_free error: 0 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.376 / SU R_free Blow DPI: 0.239 / SU R_free Cruickshank DPI: 0.242

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	1108	5.13 %	RANDOM
R_work	0.206	-	-	-
obs	0.207	21600	98.4 %	-

Displacement parameters

B_iso max: 174.89 Å² / B_iso mean: 84.34 Å² / B_iso min: 44.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.3199 Å²	0 Å²	0 Å²
2-	-	-2.0428 Å²	0 Å²
3-	-	-	-4.2771 Å²

Refine analyze

Luzzati coordinate error obs: 0.38 Å

Refinement step

Cycle: final / Resolution: 2.7→43.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3359	0	142	20	3521
B_iso mean	-	-	80.2	60.61	-
Num. residues	-	-	-	-	406

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	1270	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	97	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	506	HARMONIC	5
X-RAY DIFFRACTION	t_it	3591	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	422	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	4094	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	3591	HARMONIC	2	0.01
X-RAY DIFFRACTION	t_angle_deg	4832	HARMONIC	2	1.03
X-RAY DIFFRACTION	t_omega_torsion				2.55
X-RAY DIFFRACTION	t_other_torsion				21.22

LS refinement shell

Resolution: 2.7→2.83 Å / R_factor R_free error: 0 / Total num. of bins used: 11

	R_factor	Num. reflection	% reflection
R_free	0.257	144	5.61 %
R_work	0.244	2422	-
all	0.245	2566	-
obs	-	-	88.6 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	9.0681	1.196	-2.2882	7.0348	0.8018	5.7811	-0.3317	-0.0723	-0.8115	-0.0017	0.5185	-0.4052	0.6792	1.1608	-0.1867	0.5828	0.0375	-0.0496	0.6914	-0.6511	1.1301	43.7109	19.5723	30.8739
2	10.5264	-2.835	0.2257	1.986	0.7346	2.2706	-0.0529	1.4843	1.6051	-0.427	0.1357	0.0206	-0.1453	0.4103	-0.0827	0.4848	-0.0796	-0.1049	0.7563	-0.3051	1.1334	36.0025	33.8004	26.2221
3	15.5357	-4.0497	2.2226	0.2026	-0.0149	1.6454	-0.4868	0.0451	1.1286	0.1621	0.1161	-0.0721	-0.2431	0.3705	0.3708	0.5116	-0.0536	-0.1078	0.6624	-0.5768	1.0786	41.8101	34.2269	35.6358
4	3.5201	-2.1784	-1.3454	0.9924	1.6948	8.8303	-0.1032	-0.5111	-0.3111	0.6055	0.1228	0.53	0.1448	0.1189	-0.0196	0.7988	-0.2242	0.2785	0.7526	-0.4751	0.9189	22.9281	3.8613	26.9581
5	0.8779	-4.065	2.6589	2.286	-0.9715	0.0878	0.1624	0.4601	-0.0506	-0.7608	-0.356	0.3482	-1.4449	-0.0362	0.1936	0.6442	-0.1894	0.2318	0.6973	-0.5456	0.6941	22.8723	6.6253	6.815
6	0	-1.4662	1.5238	0.2677	0.8246	3.5981	0.1502	0.4068	-0.6041	0.1145	-0.1769	1.0173	-0.1877	-0.4402	0.0268	0.6032	-0.24	0.4428	0.696	-0.7519	1.1349	14.196	7.8785	17.9068
7	0.0845	1.4186	-2.3728	0	1.8668	8.5489	0.0634	0.1106	-0.9735	0.349	-0.36	0.7452	0.7776	-0.5457	0.2966	0.6063	-0.0972	0.1805	0.6758	-0.5832	1.29	15.0319	-2.3557	16.991
8	4.9334	3.0722	-0.7142	2.6728	-5.8306	7.9428	0.6693	-0.7858	-0.2667	0.5077	0.0343	0.5402	0.3437	0.3222	-0.7036	0.869	-0.151	0.2407	0.6189	-0.405	1.1511	22.552	-5.8468	23.8717
9	8.4468	-1.1326	-0.7997	2.9114	1.0552	5.4823	-0.3648	0.5975	-0.4551	-0.3444	-0.2432	-0.5163	0.974	0.45	0.608	0.585	-0.05	0.1686	0.5548	-0.2859	0.5773	45.3325	7.5304	12.2452
10	5.0762	0.4499	3.1386	7.784	-6.853	8.5788	0.1627	0.378	1.198	0.4052	0.0487	-0.7705	-1.0993	-0.4742	-0.2114	0.7992	0.0393	0.1134	0.5712	-0.1248	0.7553	42.4056	26.8069	9.9959
11	4.7092	1.3355	-2.2761	2.9616	0.9481	0.3348	-0.1803	0.8038	0.0646	-0.2034	0.0194	0.1856	0.1106	-0.6552	0.1609	0.6347	-0.0819	0.095	0.7279	-0.3062	0.4622	38.112	11.4955	10.8976
12	0	1.594	-3.0426	7.65	2.28	3.026	-0.2475	-1.099	-0.1496	0.9419	0.3465	-0.636	0.3999	0.5839	-0.099	0.6846	0.0835	0.0103	0.8342	-0.4556	0.6254	17.8701	26.3439	41.9621
13	0	0.0872	2.168	6.5246	3.1635	4.2967	-0.4396	-0.4131	0.4645	0.1809	-0.118	0.3844	0.1332	-0.661	0.5576	0.3467	-0.1025	0.1015	0.8714	-0.8681	0.9412	5.9078	28.3228	30.1969
14	12.3303	-0.6905	0.1792	4.321	0.9882	0.0959	0.0611	0.5493	-0.4538	-0.0491	-0.1262	-0.0824	0.5381	-0.273	0.0651	0.5043	-0.0943	0.1445	0.5422	-0.4383	0.5997	12.4844	19.5356	27.082
15	9.2045	-1.5073	3.8932	0.1897	0.4681	0.6155	-0.1305	1.2463	0.8906	-0.4397	-0.2461	-0.364	0.3314	0.517	0.3766	0.534	-0.0673	0.064	0.6588	-0.281	0.7176	17.3094	27.7439	24.1521
16	9.1037	-0.7484	6.1193	1.5447	1.4955	5.0622	-0.9121	-0.1836	0.9079	-0.1724	0.305	-0.3767	-0.5992	-0.0405	0.6071	0.5233	-0.0724	0.0185	0.6115	-0.3756	1.0347	15.5953	35.6071	31.7081

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|437 - A\|452 }	A	437 - 452
2	X-RAY DIFFRACTION	2	{ A\|453 - A\|495 }	A	453 - 495
3	X-RAY DIFFRACTION	3	{ A\|496 - A\|538 }	A	496 - 538
4	X-RAY DIFFRACTION	4	{ B\|438 - B\|459 }	B	438 - 459
5	X-RAY DIFFRACTION	5	{ B\|460 - B\|470 }	B	460 - 470
6	X-RAY DIFFRACTION	6	{ B\|471 - B\|495 }	B	471 - 495
7	X-RAY DIFFRACTION	7	{ B\|496 - B\|518 }	B	496 - 518
8	X-RAY DIFFRACTION	8	{ B\|519 - B\|538 }	B	519 - 538
9	X-RAY DIFFRACTION	9	{ C\|437 - C\|464 }	C	437 - 464
10	X-RAY DIFFRACTION	10	{ C\|465 - C\|480 }	C	465 - 480
11	X-RAY DIFFRACTION	11	{ C\|481 - C\|538 }	C	481 - 538
12	X-RAY DIFFRACTION	12	{ D\|438 - D\|452 }	D	438 - 452
13	X-RAY DIFFRACTION	13	{ D\|453 - D\|464 }	D	453 - 464
14	X-RAY DIFFRACTION	14	{ D\|465 - D\|495 }	D	465 - 495
15	X-RAY DIFFRACTION	15	{ D\|496 - D\|518 }	D	496 - 518
16	X-RAY DIFFRACTION	16	{ D\|519 - D\|538 }	D	519 - 538

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi