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- PDB-9g6u: p53-Y220C Core Domain Covalently Bound to 3,5-Dichloro-6-Ethylpyr... -

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Basic information

Entry
Database: PDB / ID: 9g6u
Titlep53-Y220C Core Domain Covalently Bound to 3,5-Dichloro-6-Ethylpyrazine-2-carbonitirle Soaked at 5 mM
ComponentsCellular tumor antigen p53
KeywordsCELL CYCLE / Covalent / SNAr / Stabilization
Function / homology
Function and homology information


negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria ...negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of thymocyte apoptotic process / positive regulation of mitochondrial membrane permeability / germ cell nucleus / regulation of fibroblast apoptotic process / bone marrow development / circadian behavior / cellular response to actinomycin D / histone deacetylase regulator activity / positive regulation of programmed necrotic cell death / : / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / T cell proliferation involved in immune response / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / negative regulation of glial cell proliferation / regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / thymocyte apoptotic process / ER overload response / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / B cell lineage commitment / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / Zygotic genome activation (ZGA) / negative regulation of mitophagy / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / necroptotic process / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / rRNA transcription / negative regulation of reactive oxygen species metabolic process / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional Regulation by VENTX / cellular response to UV-C / viral process / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / replicative senescence / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / general transcription initiation factor binding / chromosome organization / positive regulation of execution phase of apoptosis / hematopoietic stem cell differentiation / type II interferon-mediated signaling pathway / embryonic organ development / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to X-ray / hematopoietic progenitor cell differentiation / somitogenesis / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / glial cell proliferation / cellular response to glucose starvation / negative regulation of fibroblast proliferation / cis-regulatory region sequence-specific DNA binding / mitophagy / Regulation of TP53 Activity through Acetylation / negative regulation of proteolysis / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / cardiac muscle cell apoptotic process / response to salt stress / transcription repressor complex / 14-3-3 protein binding / gastrulation / positive regulation of cardiac muscle cell apoptotic process / transforming growth factor beta receptor signaling pathway / reactive oxygen species metabolic process
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsStahlecker, J. / Klett, T. / Stehle, T. / Boeckler, F.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Drug Des Devel Ther / Year: 2025
Title: S N Ar Reactive Pyrazine Derivatives as p53-Y220C Cleft Binders with Diverse Binding Modes.
Authors: Klett, T. / Stahlecker, J. / Schwer, M. / Jaag, S.J. / Masberg, B. / Knappe, C. / Lammerhofer, M. / Stehle, T. / Boeckler, F.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,22128
Polymers49,0622
Non-polymers3,15926
Water6,612367
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,06214
Polymers24,5311
Non-polymers1,53113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,15914
Polymers24,5311
Non-polymers1,62913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.816, 71.158, 105.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 24530.811 Da / Num. of mol.: 2 / Mutation: Y220C, M133L, V203A, N239Y, N268D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637

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Non-polymers , 8 types, 393 molecules

#2: Chemical
ChemComp-A1II1 / 3,5-bis(chloranyl)-6-ethyl-pyrazine-2-carbonitrile


Mass: 202.041 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H5Cl2N3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100 mM HEPES (pH = 7.2), 19 % PEG4000 and 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 58173 / % possible obs: 96.1 % / Redundancy: 9.13 % / Biso Wilson estimate: 34.64 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 7.98 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 9030 / CC1/2: 0.55 / Rrim(I) all: 2.12

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→47.92 Å / SU ML: 0.2136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 1499 2.58 %
Rwork0.1939 56553 -
obs0.1948 58052 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.87 Å2
Refinement stepCycle: LAST / Resolution: 1.64→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 152 367 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013325
X-RAY DIFFRACTIONf_angle_d1.05264508
X-RAY DIFFRACTIONf_chiral_restr0.0665484
X-RAY DIFFRACTIONf_plane_restr0.0102591
X-RAY DIFFRACTIONf_dihedral_angle_d8.9809529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.37211270.34014793X-RAY DIFFRACTION90.91
1.69-1.750.32091340.3025100X-RAY DIFFRACTION96.09
1.75-1.820.29471360.27235115X-RAY DIFFRACTION96.65
1.82-1.910.3021360.23675122X-RAY DIFFRACTION96.25
1.91-2.010.28071350.20465091X-RAY DIFFRACTION96.37
2.01-2.130.23081370.19575143X-RAY DIFFRACTION96.47
2.13-2.30.22681360.18765173X-RAY DIFFRACTION96.53
2.3-2.530.22541370.18875175X-RAY DIFFRACTION97.09
2.53-2.90.23891390.19845239X-RAY DIFFRACTION97.32
2.9-3.650.22481400.1785252X-RAY DIFFRACTION96.68
3.65-47.920.19211420.17455350X-RAY DIFFRACTION94.84
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)
10.747881088893-0.1429237724250.3307885835771.28296544928-0.07473834117191.83997105661-0.00327578329890.129653693560.121552557979-0.0316690446876-0.0915495122588-0.0583085148543-0.2143127444320.08531323540782.08960206191E-50.24833453785-0.02809805115860.002756959450940.251799246560.01339141423080.2792489013930.28111541024319.299279821531.2541807603
20.5807715860720.582540193058-0.394307473221.433519707190.5032411171081.832658667090.0001754559443480.169502602397-0.276748312871-0.008262600036660.01526910752970.06397719669720.176318581191-0.003453832331676.42862880003E-50.240780495126-0.0036375309156-0.006702170454670.254541337169-0.02051974846610.302070187391-3.483806701172.0826973561428.7442424043
31.09954619318-0.3365829139380.0225431207891.822719542830.1161798414222.824959226640.007806053084750.100015216794-0.0698124364861-0.0118983805141-0.0677543623909-0.0125688369336-0.02895135259470.0113075531751-0.0002573897299810.155833975105-0.008663732550310.0008638590598970.2170669612110.0004875076301750.233114900619-0.54624072685711.43163114530.5228987024
40.219379287118-0.0705413772951-0.008421543439290.0961911710466-0.1407304648070.2805643507240.337527057722-0.0198916564745-0.4835603065620.25850906608-0.4312400659940.1189749667210.233014569404-0.3687001159678.10665699752E-50.31341364820.01336521064040.008240109243620.309395693193-0.02663209818370.527609304874-44.734481787222.434057719836.1914018444
50.91766941594-0.001837954464440.8549520803931.66582311436-0.7016587103711.08578723441-0.04033786358370.1166812645210.0747713928765-0.186258215618-0.0430493487878-0.12938676368-0.2499342416230.123108158058.57751898525E-50.215790071744-0.009538999323520.02367632322770.1863474439670.01605845931630.213572318804-29.624146751328.286045264830.148671508
60.1710137935210.144961718682-0.6066044977052.426356557690.4014179478262.48822115148-0.004042825928460.138824499403-0.153577735485-0.1338968557960.0871776907667-0.0418109832770.142264094467-0.135707566575-6.04537931041E-50.178473632366-0.009554512085630.007436645034440.202989733687-0.0004554561272230.249318023515-33.840079608411.137190302329.9530674766
70.07128878196-0.07413933294210.1168836848990.102009891474-0.1057503851360.198070740883-0.150306958678-0.27825115638-0.4984586966920.2185599022030.1385667164570.0424661451940.2436830247810.022013524523-0.0004583230091510.267900846344-0.02710995066520.02664347813370.2914213549580.03132282870390.366973261094-37.80437849648.6379125475639.0344212811
80.503328919509-0.4955506428090.1790434758470.503869498056-0.2671469264770.5222826038-0.166739381444-0.0493883349280.658022964128-0.0954037590588-0.2203003558280.0231829371806-0.3127961363280.357329978581-0.01766692865160.314359381146-0.0580287915711-0.04880332673670.3176932900640.04493048526950.380455835556-25.650629988925.317895189540.551309364
91.18900398929-0.24577430219-0.5416466076520.895173483952-0.5758125832310.803275902877-0.2389545894920.156338989941-0.120196516988-0.5565570955390.128385387358-0.112831995754-0.22078918297-0.01673153436930.001659262746110.26788088503-0.01498792413980.01231326743260.210418811422-0.01077278039330.235543455119-32.02929341214.638835076423.4652238382
100.875556632919-0.2613116033880.3524656210822.2657641950.5248694583790.321464146771-0.01734561767790.174281607975-0.0036281488336-0.4204952896130.01125361353080.115048496144-0.095964223178-0.231783730525-0.01709816880460.2405492898170.000264343240687-0.009434593752120.2235160769750.003844531241910.193168393064-35.751573787724.373633102826.9967313547
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 95 through 155 )AA95 - 1551 - 61
22chain 'A' and (resid 156 through 194 )AA156 - 19462 - 100
33chain 'A' and (resid 195 through 291 )AA195 - 291101 - 197
44chain 'B' and (resid 94 through 104 )BN94 - 1041 - 11
55chain 'B' and (resid 105 through 155 )BN105 - 15512 - 62
66chain 'B' and (resid 156 through 203 )BN156 - 20363 - 110
77chain 'B' and (resid 204 through 213 )BN204 - 213111 - 120
88chain 'B' and (resid 214 through 229 )BN214 - 229121 - 136
99chain 'B' and (resid 230 through 250 )BN230 - 250137 - 157
1010chain 'B' and (resid 251 through 291 )BN251 - 291158 - 198

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