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- PDB-5vzs: BRD4-BD1 in complex with Cpd19 (3-(7-(difluoromethyl)-6-(1-methyl... -

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Basic information

Entry
Database: PDB / ID: 5vzs
TitleBRD4-BD1 in complex with Cpd19 (3-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-N-methyl-1-(tetrahydro-2H-pyran-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide)
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION REGULATOR/INHIBITOR / BRD4 / Bromodomain / small molecule inhibitor / TRANSCRIPTION REGULATOR-INHIBITOR complex
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9U4 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.707 Å
AuthorsMurray, J.M.
CitationJournal: To be published
Title: GNE-781, A Highly Advanced Potent and Selective Bromodomain Inhibitor of CBP/P300
Authors: Murray, J.M.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6527
Polymers37,4142
Non-polymers1,2375
Water2,558142
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2953
Polymers18,7071
Non-polymers5882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3574
Polymers18,7071
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.986, 41.878, 59.895
Angle α, β, γ (deg.)102.080, 106.790, 89.360
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 18707.248 Da / Num. of mol.: 2 / Fragment: BRD4 Bromodomain-1, UNP residues 42-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9U4 / 3-[7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-N-methyl-1-(oxan-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide


Mass: 525.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33F2N7O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 20% PEG 3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→29.227 Å / Num. obs: 28278 / % possible obs: 96.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.97 Å2 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2666 / % possible all: 89.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
Aimlessdata scaling
PHENIXdev_2747refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: pdbid 5KU3

5ku3


Resolution: 1.707→29.227 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.35
RfactorNum. reflection% reflection
Rfree0.2262 1427 5.06 %
Rwork0.1922 --
obs0.194 28201 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.93 Å2 / Biso mean: 33.1643 Å2 / Biso min: 16.68 Å2
Refinement stepCycle: final / Resolution: 1.707→29.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 88 142 2352
Biso mean--32.78 38.16 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072284
X-RAY DIFFRACTIONf_angle_d0.9223114
X-RAY DIFFRACTIONf_chiral_restr0.048321
X-RAY DIFFRACTIONf_plane_restr0.006399
X-RAY DIFFRACTIONf_dihedral_angle_d12.7551363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7069-1.76790.36451200.33132363248383
1.7679-1.83870.34291290.29762602273193
1.8387-1.92240.31721490.26652672282195
1.9224-2.02370.27061640.23652681284597
2.0237-2.15040.2591380.20642746288496
2.1504-2.31640.23891140.20242767288197
2.3164-2.54940.24251540.21122729288398
2.5494-2.9180.23991290.20762755288498
2.918-3.67530.21751760.17792742291898
3.6753-29.23150.18221540.14882717287197
Refinement TLS params.Method: refined / Origin x: -1.589 Å / Origin y: 3.5262 Å / Origin z: 31.0582 Å
111213212223313233
T0.2028 Å2-0.0068 Å2-0.017 Å2-0.2078 Å20.023 Å2--0.2173 Å2
L0.7687 °2-0.6988 °2-0.9369 °2-0.7252 °21.2064 °2--2.0186 °2
S-0.0407 Å °0.0869 Å °-0.0365 Å °0.0092 Å °-0.0796 Å °0.0285 Å °0.044 Å °-0.1869 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 168
2X-RAY DIFFRACTION1allB42 - 168
3X-RAY DIFFRACTION1allM1 - 142
4X-RAY DIFFRACTION1allS1 - 3
5X-RAY DIFFRACTION1allY1
6X-RAY DIFFRACTION1allZ1

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