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- PDB-9ht1: A novel bottom-up approach to find lead-compounds in billion-size... -

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Basic information

Entry
Database: PDB / ID: 9ht1
TitleA novel bottom-up approach to find lead-compounds in billion-sized libraries
ComponentsBromodomain-containing protein 4
KeywordsGENE REGULATION / BRD4 / drug discovery
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsRuiz Carrillo, D. / Garcia Alai, M. / Barril, X. / Serrano-Morras, A. / Bertran-Mostazo, A. / Juarez-Jimenez, J. / Defelipe, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)CEX2021-001202-M Spain
CitationJournal: Commun Chem / Year: 2025
Title: A bottom-up approach to find lead compounds in expansive chemical spaces.
Authors: Serrano-Morras, A. / Bertran-Mostazo, A. / Minarro-Lleonar, M. / Comajuncosa-Creus, A. / Cabello, A. / Labranya, C. / Escudero, C. / Tian, T.V. / Khutorianska, I. / Radchenko, D.S. / Moroz, ...Authors: Serrano-Morras, A. / Bertran-Mostazo, A. / Minarro-Lleonar, M. / Comajuncosa-Creus, A. / Cabello, A. / Labranya, C. / Escudero, C. / Tian, T.V. / Khutorianska, I. / Radchenko, D.S. / Moroz, Y.S. / Defelipe, L. / Ruiz-Carrillo, D. / Garcia-Alai, M. / Schmidt, R. / Rarey, M. / Aloy, P. / Galdeano, C. / Juarez-Jimenez, J. / Barril, X.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)30,8704
Polymers30,1992
Non-polymers6712
Water3,459192
1
A: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)15,0991
Polymers15,0991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7703
Polymers15,0991
Non-polymers6712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.989, 79.035, 84.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15099.380 Da / Num. of mol.: 2
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-A1IXE / 1-(2,8-dioxa-5-azaspiro[3.6]decan-5-yl)-2-[[5-methyl-4-(4-methylphenyl)-1,2,4-triazol-3-yl]sulfanyl]ethanone


Mass: 388.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus 0.1 Amino acids, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant Mix 1

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97702 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 1.94→57.62 Å / Num. obs: 21437 / % possible obs: 99.95 % / Redundancy: 13.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.04064 / Rrim(I) all: 0.1478 / Net I/σ(I): 12.97
Reflection shellResolution: 1.94→2.009 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.099 / Num. unique obs: 2127 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.3088 / Rrim(I) all: 1.142 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC1.19.2-4158refinement
PDB-REDO4.4.7refinement
MxCuBEdata collection
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→57.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.772 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22164 1033 4.8 %RANDOM
Rwork0.17783 ---
obs0.17995 20397 99.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.793 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-0 Å20 Å2
2--1.13 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.94→57.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 46 192 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0182232
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162126
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.8423032
X-RAY DIFFRACTIONr_angle_other_deg0.51.5984927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535.116258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75510394
X-RAY DIFFRACTIONr_chiral_restr0.070.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_mcbond_it3.3011.5521014
X-RAY DIFFRACTIONr_mcbond_other3.2771.5511014
X-RAY DIFFRACTIONr_mcangle_it3.8462.7561264
X-RAY DIFFRACTIONr_mcangle_other3.8442.7611265
X-RAY DIFFRACTIONr_scbond_it6.2992.1381218
X-RAY DIFFRACTIONr_scbond_other6.2982.141219
X-RAY DIFFRACTIONr_scangle_other8.8343.6521767
X-RAY DIFFRACTIONr_long_range_B_refined10.6218.422617
X-RAY DIFFRACTIONr_long_range_B_other10.64217.472558
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 65 -
Rwork0.235 1517 -
obs--99.87 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.3652-5.3064-2.35875.4211.94662.7490.21450.04270.1906-0.2131-0.1037-0.1073-0.01690.009-0.11090.0736-0.0170.00850.0236-0.01560.057631.3144.23-8.334
24.76421.2664-1.63399.5497-4.38863.3218-0.06810.29870.45210.25270.14090.1834-0.4922-0.0808-0.07290.1589-0.0228-0.04220.1181-0.01470.111611.72211.8-2.292
36.699-1.3453-4.89721.14180.76365.0883-0.0351-0.5068-0.05790.09470.0039-0.00850.20080.29440.03130.083-0.0245-0.02460.07050.00360.033424.308-5.8740.915
44.4835-2.5683-1.36632.72191.04660.79170.05870.05980.186-0.0413-0.0473-0.0299-0.0131-0.0703-0.01140.04220.0015-0.01430.0194-0.00480.040622.0133.09-7.053
55.9052-5.7477-1.15599.17421.85571.84120.10790.2201-0.1515-0.2376-0.19450.4097-0.0515-0.26230.08660.0614-0.0191-0.02280.05240.00230.039616.788-3.767-9.094
611.0756-5.8615-3.34697.30092.92963.02690.0851-0.032-0.2424-0.146-0.14270.40930.0452-0.28780.05770.1074-0.0594-0.03040.07280.00880.044812.447-9.015-2.736
79.5095-9.2266-0.912.62240.10225.02920.22780.39760.2624-0.1452-0.3825-0.5892-0.00770.17520.15470.0704-0.0117-0.01830.03510.01410.125730.39224.70916.397
812.07335.50470.12717.5271-0.30820.03090.3225-0.6559-0.07940.2632-0.2810.3660.0072-0.0064-0.04150.1032-0.0423-0.01460.073-0.01170.085714.837.47117.777
94.082-4.65922.13288.4336-3.65984.0234-0.0442-0.14570.13420.25570.16390.3118-0.2552-0.0562-0.11970.066-0.00910.03820.03150.00320.09838.39823.09625.114
107.1161-0.7176-1.61739.23270.98755.745-0.254-0.3466-0.28930.31830.12690.2170.1866-0.19310.12710.05280.02450.01150.03950.01210.019817.0349.91625.994
118.1053-1.85470.58143.2163-0.07550.0507-0.0242-0.42850.09150.05040.0324-0.34270.0183-0.012-0.00810.09860.0156-0.01820.10160.00020.091531.45413.38419.059
123.7047-2.8373-0.93134.60261.58692.81530.0879-0.09150.2134-0.00470.0889-0.2502-0.2150.1904-0.17670.0437-0.0288-0.00620.02230.00570.075823.00921.19316.685
131.9497-3.5214-0.40158.47481.07380.51220.06060.0773-0.0496-0.0503-0.03210.3294-0.0158-0.0367-0.02850.0566-0.01950.00680.03890.02110.068816.25618.73713.491
1414.3489-8.9436-0.10279.48011.01622.5340.09850.08540.0733-0.1418-0.0370.3671-0.1637-0.2675-0.06150.0815-0.01370.00650.0550.0280.06598.14114.0118.6
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 51
2X-RAY DIFFRACTION2A52 - 68
3X-RAY DIFFRACTION3A69 - 96
4X-RAY DIFFRACTION4A97 - 121
5X-RAY DIFFRACTION5A122 - 139
6X-RAY DIFFRACTION6A140 - 168
7X-RAY DIFFRACTION7B42 - 51
8X-RAY DIFFRACTION8B52 - 60
9X-RAY DIFFRACTION9B61 - 75
10X-RAY DIFFRACTION10B76 - 83
11X-RAY DIFFRACTION11B84 - 96
12X-RAY DIFFRACTION12B97 - 116
13X-RAY DIFFRACTION13B117 - 144
14X-RAY DIFFRACTION14B145 - 168

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