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- PDB-24kk: Crystal structure of the second bromodomain (BD2) of human BRD2 i... -

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Basic information

Entry
Database: PDB / ID: 24kk
TitleCrystal structure of the second bromodomain (BD2) of human BRD2 in complex with Mefanamic acid
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / Inhibitor
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / histone H3K14ac reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / neural tube closure / protein localization to chromatin / nucleosome assembly ...acetylation-dependent protein binding / chromatin looping / histone H3K14ac reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / neural tube closure / protein localization to chromatin / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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
2-[(2,3-DIMETHYLPHENYL)AMINO]BENZOIC ACID / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPadmanabhan, B. / Ashok, S.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical Research(No. 2021-9152) India
CitationJournal: Proteins / Year: 2026
Title: BET Bromodomain Targeting by NSAIDs: Structural, Biophysical, and Computational Insights.
Authors: Sridhar, A. / Kandhasami, N. / Mathur, S. / Krishnappa, G. / Thiyagarajan, S. / Padmanabhan, B.
History
DepositionMar 6, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5332
Polymers13,2911
Non-polymers2411
Water3,837213
1
A: Bromodomain-containing protein 2
hetero molecules

A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0654
Polymers26,5822
Non-polymers4832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)52.494, 71.838, 32.167
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-740-

HOH

21A-749-

HOH

31A-813-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1


Mass: 13291.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25440
#2: Chemical ChemComp-ID8 / 2-[(2,3-DIMETHYLPHENYL)AMINO]BENZOIC ACID / MEFENAMIC ACID


Mass: 241.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG MME 2000, 50mM Tris, 50mM NaCl

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 18, 2025
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.2→27.43 Å / Num. obs: 38722 / % possible obs: 99.4 % / Redundancy: 6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.083 / Net I/σ(I): 31
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 1865 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VRM

7vrm


Resolution: 1.2→27.43 Å / SU ML: 0.1194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 1933 5 %
Rwork0.1718 36715 -
obs0.173 38648 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.26 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 18 213 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611049
X-RAY DIFFRACTIONf_angle_d0.91251424
X-RAY DIFFRACTIONf_chiral_restr0.0758136
X-RAY DIFFRACTIONf_plane_restr0.0063199
X-RAY DIFFRACTIONf_dihedral_angle_d4.1796169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.2791330.27522514X-RAY DIFFRACTION96.96
1.23-1.260.27691330.22942561X-RAY DIFFRACTION99.04
1.26-1.30.21981360.21422571X-RAY DIFFRACTION99.34
1.3-1.340.23311380.19342625X-RAY DIFFRACTION99.28
1.34-1.390.20171350.1822568X-RAY DIFFRACTION99.41
1.39-1.450.21821370.17132590X-RAY DIFFRACTION99.89
1.45-1.510.19311370.16582607X-RAY DIFFRACTION99.82
1.51-1.590.20351380.15862621X-RAY DIFFRACTION99.78
1.59-1.690.17981390.1582644X-RAY DIFFRACTION99.89
1.69-1.820.20161370.16522605X-RAY DIFFRACTION99.96
1.82-20.20051400.17392649X-RAY DIFFRACTION99.82
2.01-2.290.18161410.15982668X-RAY DIFFRACTION99.82
2.29-2.890.18321410.16662681X-RAY DIFFRACTION99.89
2.89-27.430.18521480.16852811X-RAY DIFFRACTION99.26
Refinement TLS params.

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

IDL11 (°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)
11.205094943020.0208268352712-0.7280807904961.78648533030.2373164163170.670854304681-0.04291136055480.1073393697250.0723983850125-0.0505881523760.01187389634890.0816476592859-0.1094443048710.00476703448161-0.003339997073670.0775470054792-0.0191441631492-0.004678186833460.0778988122501-0.007960787240540.07944663836768.5769027533211.40494340980.618017519886
20.20028480795-0.167701884203-0.2313034513750.562050299575-0.07093580996830.2853292913620.01878235538220.0409937305285-0.0251330212238-0.0454678206041-0.0240501372521-0.2254890347070.02589932998370.06272847305011.4161180504E-50.1014699336240.0116624973043-0.01209531388890.0992386362686-0.003343615971720.14071584603218.8796314461-8.05687738640.580402349979
30.344434344075-0.551031264070.01029554168740.978778581844-0.04446108559550.0429517390608-0.04361993118670.2082871946860.0256763294243-0.340676655332-0.041060593196-0.03949620527450.0146556980555-0.033093197376-0.01169756938870.128375149298-0.0159437462380.01059989374140.126083137782-0.002677430418610.10129983412415.22248128817.35476841462-6.13786702769
40.840185692293-0.0438918541226-0.2869803270560.7329701565690.3243237712190.2944388854880.01639837943040.128424164485-0.00804031693559-0.11173151838-0.01053425146390.0244485044615-0.06284829678140.024986490664-8.11538241975E-50.108220862054-0.00138505540637-0.002163407295520.10806638989-0.003904569106550.09805609895147.575903088192.00070489982-5.09862255471
51.28675106470.555301084036-0.4440029542730.9776020750690.351121350520.7108944958130.00542170404501-0.0890985464092-0.01897060882980.1172291237120.01543482822430.0481449437485-0.01114166671810.01613187766040.0003836898336050.0892479305849-0.00444983484335-0.001065355209630.0928201044609-0.008339383449880.07390943109854.784228940552.447552982597.7719002279
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 341 through 372 )341 - 3721 - 32
22chain 'A' and (resid 373 through 395 )373 - 39533 - 55
33chain 'A' and (resid 396 through 404 )396 - 40456 - 64
44chain 'A' and (resid 405 through 428 )405 - 42865 - 88
55chain 'A' and (resid 429 through 454 )429 - 45489 - 114

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