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- PDB-9ht2: A novel bottom-up approach to find lead-compounds in billion-size... -

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Basic information

Entry
Database: PDB / ID: 9ht2
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
: / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6323
Polymers15,0991
Non-polymers5332
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint5 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.353, 39.553, 55.861
Angle α, β, γ (deg.)90.000, 105.492, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15099.380 Da / Num. of mol.: 1
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-A1IXF / methyl 2,2,6,6-tetramethyl-4-[[2-[(5-methyl-1,3,4-thiadiazol-2-yl)amino]-2-oxidanylidene-ethyl]amino]oxane-4-carboxylate


Mass: 370.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus 0.09 M Halogens, 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: 1.42→26.93 Å / Num. obs: 23321 / % possible obs: 95.93 % / Redundancy: 7.1 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.07624 / Rpim(I) all: 0.03085 / Rrim(I) all: 0.08237 / Net I/σ(I): 13.07
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 7 % / Rmerge(I) obs: 0.6479 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2271 / CC1/2: 0.838 / CC star: 0.955 / Rpim(I) all: 0.262 / Rrim(I) all: 0.6998 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2.4158refinement
PDB-REDOrefinement
MxCuBE4.4.7data collection
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→26.93 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.337 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.065 / 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
Rfree0.18634 1215 5.2 %RANDOM
Rwork0.17173 ---
obs0.1725 22157 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.278 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.54 Å2
2---1.18 Å2-0 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.42→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 36 156 1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0181128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161082
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.8611535
X-RAY DIFFRACTIONr_angle_other_deg0.4511.6192501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865.116129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30510197
X-RAY DIFFRACTIONr_chiral_restr0.0520.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_mcbond_it4.4640.865507
X-RAY DIFFRACTIONr_mcbond_other4.3250.865507
X-RAY DIFFRACTIONr_mcangle_it4.4181.525632
X-RAY DIFFRACTIONr_mcangle_other4.4171.533633
X-RAY DIFFRACTIONr_scbond_it7.5431.43621
X-RAY DIFFRACTIONr_scbond_other7.5411.433622
X-RAY DIFFRACTIONr_scangle_other8.6452.377904
X-RAY DIFFRACTIONr_long_range_B_refined9.5913.071348
X-RAY DIFFRACTIONr_long_range_B_other9.65111.431301
LS refinement shellResolution: 1.42→1.456 Å
RfactorNum. reflection% reflection
Rfree0.313 80 -
Rwork0.27 1590 -
obs--93.24 %
Refinement TLS params.Method: refined / Origin x: -1.87 Å / Origin y: 3.218 Å / Origin z: 12.392 Å
111213212223313233
T0.0636 Å20.0158 Å20.0194 Å2-0.1481 Å20.0135 Å2--0.0133 Å2
L1.8912 °20.1884 °2-0.7605 °2-1.0904 °20.1711 °2--1.5661 °2
S0.0504 Å °0.0416 Å °0.0674 Å °-0.024 Å °-0.0599 Å °-0.0544 Å °-0.0667 Å °-0.0204 Å °0.0094 Å °

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