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- PDB-6dmk: A multiconformer ligand model of an isoxazolyl-benzimidazole liga... -

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Basic information

Entry
Database: PDB / ID: 6dmk
TitleA multiconformer ligand model of an isoxazolyl-benzimidazole ligand bound to the bromodomain of human CREBBP
ComponentsCREB-binding protein
Keywordstranscription/transcription inhibitor / Complex / multi conformer model / TRANSCRIPTION / transcription-transcription inhibitor complex
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...peptide lactyltransferase (CoA-dependent) activity / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / embryonic digit morphogenesis / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / negative regulation of transcription by RNA polymerase I / RUNX3 regulates NOTCH signaling / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of NFE2L2 gene expression / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / TRAF6 mediated IRF7 activation / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / histone acetyltransferase activity / regulation of nucleotide-excision repair / FOXO-mediated transcription of cell death genes / positive regulation of transforming growth factor beta receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / Attenuation phase / protein-lysine-acetyltransferase activity / cAMP/PKA signal transduction / histone acetyltransferase / canonical NF-kappaB signal transduction / positive regulation of double-strand break repair via homologous recombination / regulation of cellular response to heat / cellular response to nutrient levels / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian expression / Transcriptional and post-translational regulation of MITF-M expression and activity / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / CD209 (DC-SIGN) signaling / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / protein destabilization / positive regulation of protein localization to nucleus / Transcriptional regulation of white adipocyte differentiation / chromatin DNA binding / Formation of the beta-catenin:TCF transactivating complex / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / tau protein binding / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / p53 binding / cellular response to UV / transcription corepressor activity / rhythmic process / Regulation of PD-L1(CD274) transcription / transcription regulator complex / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / TRAF3-dependent IRF activation pathway / DNA-binding transcription factor binding / Estrogen-dependent gene expression / response to hypoxia / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA-templated transcription
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetyltransferase KAT11-type domain / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2LL / NITRATE ION / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.66 Å
AuthorsHudson, B.M. / van Zundert, G. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
CitationJournal: J. Med. Chem. / Year: 2018
Title: qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
Authors: van Zundert, G.C.P. / Hudson, B.M. / de Oliveira, S.H.P. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 1, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name
Remark 0THIS ENTRY 6DMK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4NR5, DETERMINED BY P. ...THIS ENTRY 6DMK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4NR5, DETERMINED BY P.FILIPPAKOPOULOS,S.PICAUD,I.FELLETAR,D.HAY,O.FEDOROV,S.MARTIN,A.W.PIKE,F.VON DELFT,P.BRENNAN,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1034
Polymers13,5481
Non-polymers5553
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.697, 44.311, 52.916
Angle α, β, γ (deg.)90.000, 95.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CREB-binding protein


Mass: 13548.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-2LL / 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazole


Mass: 430.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.13 Å3/Da / Density % sol: 42.14 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 4NR5
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M NaNO3, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.66→19.3 Å / Num. obs: 13513 / % possible obs: 99.7 % / Redundancy: 3.3 % / Net I/σ(I): 17
Reflection shellResolution: 1.66→1.75 Å

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Processing

Software
NameVersionClassification
PHENIX1.11_2558refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.66→19.298 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.17
RfactorNum. reflection% reflection
Rfree0.2339 645 4.93 %
Rwork0.1997 --
obs0.2015 13079 96.58 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Displacement parametersBiso max: 86.23 Å2 / Biso mean: 38.8892 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: final / Resolution: 1.66→19.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 138 80 1144
Biso mean--33.35 34.76 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151031
X-RAY DIFFRACTIONf_angle_d1.3841403
X-RAY DIFFRACTIONf_chiral_restr0.061138
X-RAY DIFFRACTIONf_plane_restr0.011175
X-RAY DIFFRACTIONf_dihedral_angle_d15.682603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.66-1.78810.30521210.27632494261598
1.7881-1.96790.29961270.23622473260097
1.9679-2.25230.27941390.19922475261496
2.2523-2.83620.24231280.2182503263197
2.8362-19.29920.20321300.17972489261995

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