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- PDB-5ktw: CREBBP bromodomain in complex with Cpd 44 (3-((5-acetyl-1-(cyclop... -

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Open data


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Basic information

Entry
Database: PDB / ID: 5ktw
TitleCREBBP bromodomain in complex with Cpd 44 (3-((5-acetyl-1-(cyclopropylmethyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl)amino)-N-isopropylbenzamide)
ComponentsCREB-binding protein
KeywordsTRANSFERASE / CREBBP bromodomain
Function / homology
Function and homology information


Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes ...Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Nuclear events mediated by NFE2L2 / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / protein acetylation / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell death genes / homeostatic process / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase activity / histone acetyltransferase complex / protein-lysine-acetyltransferase activity / canonical NF-kappaB signal transduction / cAMP/PKA signal transduction / Attenuation phase / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / regulation of cellular response to heat / histone acetyltransferase / positive regulation of double-strand break repair via homologous recombination / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / cellular response to nutrient levels / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Formation of the beta-catenin:TCF transactivating complex / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / protein destabilization / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / tau protein binding / transcription coactivator binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / p53 binding / cellular response to UV / transcription corepressor activity / rhythmic process / 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 / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to hypoxia / transcription coactivator activity / nuclear body / 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 / signal transduction / positive regulation of transcription by RNA polymerase II
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 acetylation protein / 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-6XG / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.087 Å
AuthorsMurray, J.M. / Boenig, G.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Discovery of a Potent and Selective in Vivo Probe (GNE-272) for the Bromodomains of CBP/EP300.
Authors: Crawford, T.D. / Romero, F.A. / Lai, K.W. / Tsui, V. / Taylor, A.M. / de Leon Boenig, G. / Noland, C.L. / Murray, J. / Ly, J. / Choo, E.F. / Hunsaker, T.L. / Chan, E.W. / Merchant, M. / ...Authors: Crawford, T.D. / Romero, F.A. / Lai, K.W. / Tsui, V. / Taylor, A.M. / de Leon Boenig, G. / Noland, C.L. / Murray, J. / Ly, J. / Choo, E.F. / Hunsaker, T.L. / Chan, E.W. / Merchant, M. / Kharbanda, S. / Gascoigne, K.E. / Kaufman, S. / Beresini, M.H. / Liao, J. / Liu, W. / Chen, K.X. / Chen, Z. / Conery, A.R. / Cote, A. / Jayaram, H. / Jiang, Y. / Kiefer, J.R. / Kleinheinz, T. / Li, Y. / Maher, J. / Pardo, E. / Poy, F. / Spillane, K.L. / Wang, F. / Wang, J. / Wei, X. / Xu, Z. / Xu, Z. / Yen, I. / Zawadzke, L. / Zhu, X. / Bellon, S. / Cummings, R. / Cochran, A.G. / Albrecht, B.K. / Magnuson, S.
History
DepositionJul 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CREB-binding protein
B: CREB-binding protein
C: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,31914
Polymers40,6363
Non-polymers1,68311
Water10,683593
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1275
Polymers13,5451
Non-polymers5824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1275
Polymers13,5451
Non-polymers5824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0654
Polymers13,5451
Non-polymers5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.614, 44.395, 66.811
Angle α, β, γ (deg.)90.000, 106.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CREB-binding protein


Mass: 13545.468 Da / Num. of mol.: 3 / Fragment: bromodomain (UNP residues 1085-1196)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-6XG / 3-[[1-(cyclopropylmethyl)-5-ethanoyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]amino]-~{N}-propan-2-yl-benzamide


Mass: 395.498 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H29N5O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris pH 5.5, 5% v/v ethylene glycol, 23% PEG 3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.087→44.395 Å / Num. obs: 137643 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 13.2 / Num. measured all: 486509
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.087-1.0913.40.53195.2
5.045-44.3953.30.037192.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1492refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.087→36.489 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 16.27
RfactorNum. reflection% reflection
Rfree0.1758 6903 5.02 %
Rwork0.1625 --
obs0.1632 137612 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.23 Å2 / Biso mean: 15.0416 Å2 / Biso min: 3.97 Å2
Refinement stepCycle: final / Resolution: 1.087→36.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 119 594 3575
Biso mean--11.21 25.71 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123046
X-RAY DIFFRACTIONf_angle_d1.5634151
X-RAY DIFFRACTIONf_chiral_restr0.072424
X-RAY DIFFRACTIONf_plane_restr0.011536
X-RAY DIFFRACTIONf_dihedral_angle_d13.7621151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0874-1.09980.2272090.22734256446596
1.0998-1.11270.24512180.20994264448296
1.1127-1.12630.20942120.20834267447996
1.1263-1.14050.20392310.19414258448996
1.1405-1.15550.20342390.1934255449497
1.1555-1.17140.18482390.18844293453297
1.1714-1.18810.18842220.17854280450297
1.1881-1.20580.18992170.17594281449897
1.2058-1.22470.1982370.17534333457097
1.2247-1.24480.18212310.16944307453897
1.2448-1.26620.18822440.16994354459898
1.2662-1.28920.18392200.16364313453398
1.2892-1.3140.16182220.16074376459898
1.314-1.34090.17072300.16084340457098
1.3409-1.370.19472330.15684373460698
1.37-1.40190.17222550.15584339459498
1.4019-1.4370.17942250.16044389461499
1.437-1.47580.16952260.14814405463199
1.4758-1.51920.15772050.1444442464799
1.5192-1.56830.16412340.13924387462199
1.5683-1.62430.14352180.13554422464099
1.6243-1.68940.1652530.14684408466199
1.6894-1.76620.1642500.15164412466299
1.7662-1.85940.17382550.15264429468499
1.8594-1.97580.1672410.15494386462799
1.9758-2.12840.16582300.14954460469099
2.1284-2.34250.16922180.14964422464099
2.3425-2.68140.16782460.16424441468799
2.6814-3.37790.16562300.16184483471399
3.3779-36.50940.19162130.17644334454794
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)
12.39840.44570.03441.0633-0.09680.7604-0.07130.28420.0294-0.10890.0504-0.1392-0.10340.20420.01710.0874-0.0280.01090.15140.00650.0562-19.851810.88-15.0547
23.28211.01120.60852.3040.22082.7434-0.0771-0.06960.11190.09120.03030.2207-0.0829-0.22760.05580.06090.0206-0.00410.05550.01590.0688-39.251611.7112-7.514
31.83660.92190.01630.9242-0.93221.9926-0.23940.38790.3733-0.2080.19730.0513-0.29330.15540.09490.1181-0.0384-0.01030.14440.05240.115-21.34419.543-14.757
43.51871.6808-0.74811.72-0.49541.26640.03130.01630.09810.00310.00120.0017-0.06620.0971-0.03170.0542-0.0032-0.00010.04750.00050.0414-24.555512.3085-4.13
54.0242-0.6848-1.08546.233-1.12455.08130.0092-0.1402-0.04920.30590.0420.27260.0584-0.1049-0.01280.069-0.0066-0.00450.04910.00190.053-35.2849-1.3572-0.959
66.2453.08830.13932.08110.11460.82990.00420.1227-0.12090.00780.0437-0.1281-0.01540.198-0.03210.04940.0024-0.00370.073-0.00810.0519-18.4034.7588-6.208
71.55410.8294-0.05661.1596-0.05980.9764-0.0870.1229-0.0308-0.0650.0707-0.1412-0.10950.15720.00730.0683-0.0277-0.00070.0865-0.00130.051-8.035610.85995.8307
82.76310.5407-0.05982.07730.06643.0603-0.0228-0.08250.10280.06270.01430.2334-0.0239-0.31380.03730.04930.01330.00180.06470.00610.0706-26.548511.624514.395
92.57811.3297-0.08312.9365-0.05822.1522-0.03960.13640.1372-0.08060.0783-0.0553-0.30870.1302-0.00520.0863-0.0210.00560.06820.00560.0515-9.619719.37466.2787
102.22751.5044-0.7061.835-0.5631.36580.0738-0.0850.02970.072-0.0472-0.0105-0.13890.1144-0.03640.0627-0.0102-0.00430.0557-0.00580.0432-11.824812.465317.0984
111.96220.28910.22382.8386-0.84882.6055-0.0438-0.158-0.01340.1880.11220.0575-0.0016-0.1519-0.09060.0722-0.0021-0.00590.06210.01090.0594-22.0192-1.127821.3049
125.60792.9211-0.42872.0322-0.29281.0955-0.01220.0248-0.1155-0.01490.0068-0.1817-0.01810.2325-0.00650.0453-0.0038-0.00060.0783-0.00480.0681-5.585.090214.8297
132.28392.4713-0.23186.3351-1.2720.4544-0.02580.17920.2124-0.26440.0855-0.1898-0.15330.2919-0.0190.1226-0.04920.03770.158-0.01710.137610.940617.346525.1466
145.0042-2.0308-1.35073.86140.7292.8572-0.04140.1588-0.1232-0.13060.0467-0.07560.15760.07010.00060.0627-0.0129-0.00270.0475-0.00970.0401-2.08184.292327.2169
152.75910.9509-0.10912.79080.37052.6661-0.0043-0.08840.03710.09210.00980.33430.0217-0.20120.02230.05240.00770.00680.04820.01850.0888-12.532711.383835.8145
161.45831.4425-0.48654.74970.06061.97620.02360.07470.1774-0.19190.1035-0.0006-0.20540.0893-0.09390.0826-0.02090.02780.083-0.00230.07893.003820.081326.4834
172.06071.399-0.78962.8729-0.82271.87350.0486-0.026-0.01480.04470.0168-0.1301-0.01960.1224-0.05980.0509-0.0009-0.00410.0519-0.01290.04952.12512.876737.4018
183.1222-1.0779-1.92522.4825-3.02117.6417-0.0792-0.0323-0.04410.23020.17050.05040.2012-0.0463-0.01770.1154-0.0161-0.02010.04180.00450.0574-7.1287-1.633541.4868
194.30242.6274-0.90232.6877-0.7651.32450.07-0.0247-0.21640.13650.0005-0.41770.09480.3130.01920.06190.0178-0.01040.1117-0.02980.13078.50715.877234.8111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1083 through 1116 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1117 through 1134 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1135 through 1149 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1150 through 1167 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1168 through 1172 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1173 through 1196 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1083 through 1116 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1117 through 1134 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1135 through 1149 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1150 through 1167 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1168 through 1172 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1173 through 1196 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 1083 through 1102 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1103 through 1116 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 1117 through 1134 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 1135 through 1149 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 1150 through 1167 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 1168 through 1172 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 1173 through 1196 )C0

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