BMRB Entry 36163

Name: Solution NMR structures of BRD4 first bromodomain with small compound MMQO
Published: 2018-03-02

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PDB ID: 5z9c
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR36163
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structures of BRD4 first bromodomain with small compound MMQO

Deposition date:

2018-02-02

Original release date:

2018-03-02

Authors:

Zeng, L.; Zhou, M.

Citation:

Citation: Abner, E.; Stoszko, E.; Zeng, L.; Chen, H.; Izquierdo-Bouldstridge, A.; Konuma, T.; Zorita, E.; Fanunza, E.; Zhang, Q.; Mahmoudi, T.; Zhou, M.; Filion, G.; Jordon, A.. "A new quinoline BRD4 inhibitor targets a distinct latent HIV-1 reservoir for re-activation from other 'shock' drugs" J. Virol. 92, e02056-17-e02056-17 (2018).
PubMed: 29343578

Assembly members:

Assembly members:
Bromodomain-containing protein 4, polymer, 116 residues, 13947.143 Da.
8-methoxy-6-methylquinolin-4(1H)-one, non-polymer, 189.211 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Bromodomain-containing protein 4: PNKPKRQTNQLQYLLRVVLK TLWKHQFAWPFQQPVDAVKL NLPDYYKIIKTPMDMGTIKK RLENNYYWNAQECIQDFNTM FTNCYIYNKPGDDIVLMAEA LEKLFLQKINELPTEE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	449
15N chemical shifts	124
1H chemical shifts	864

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_MQO	2

Entities:

Entity 1, entity_1 116 residues - 13947.143 Da.

1

PRO

ASN

LYS

PRO

LYS

ARG

GLN

THR

ASN

GLN

2

LEU

GLN

TYR

LEU

ARG

VAL

LEU

LYS

3

THR

LEU

TRP

LYS

HIS

GLN

PHE

ALA

TRP

PRO

4

PHE

GLN

PRO

VAL

ASP

ALA

VAL

LYS

LEU

5

ASN

LEU

PRO

ASP

TYR

LYS

ILE

LYS

6

THR

PRO

MET

ASP

MET

GLY

THR

ILE

LYS

7

ARG

LEU

GLU

ASN

TYR

TRP

ASN

ALA

8

GLN

GLU

CYS

ILE

GLN

ASP

PHE

ASN

THR

MET

9

PHE

THR

ASN

CYS

TYR

ILE

TYR

ASN

LYS

PRO

10

GLY

ASP

ILE

VAL

LEU

MET

ALA

GLU

ALA

11

LEU

GLU

LYS

LEU

PHE

LEU

GLN

LYS

ILE

ASN

12

GLU

LEU

PRO

THR

GLU

Entity 2, entity_MQO - C11 H11 N O2 - 189.211 Da.

1

MQO

Samples:

sample_1: Bromodomain-containing protein 4, [U-13C; U-15N], 0.5 mM; NaCl 100 mM; sodium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 13C NOESY	sample_1	isotropic	sample_conditions_1
3D 13 NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - refinement

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks