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- PDB-9n3l: Co-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112 -

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Basic information

Entry
Database: PDB / ID: 9n3l
TitleCo-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / PCNA / transcription-replication conflict / DNA replication stress / DNA repair / HSP90alpha / HSP90
Function / homology
Function and homology information


dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / Polymerase switching / Processive synthesis on the lagging strand / MutLalpha complex binding / PCNA complex / Telomere C-strand (Lagging Strand) Synthesis ...dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / Polymerase switching / Processive synthesis on the lagging strand / MutLalpha complex binding / PCNA complex / Telomere C-strand (Lagging Strand) Synthesis / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / replisome / Processive synthesis on the C-strand of the telomere / response to L-glutamate / Removal of the Flap Intermediate from the C-strand / response to dexamethasone / DNA polymerase processivity factor activity / histone acetyltransferase binding / leading strand elongation / G1/S-Specific Transcription / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / Translesion synthesis by REV1 / positive regulation of DNA repair / nuclear estrogen receptor binding / replication fork / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / male germ cell nucleus / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / cellular response to xenobiotic stimulus / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / damaged DNA binding / chromosome, telomeric region / nuclear body / chromatin binding / centrosome / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / :
Similarity search - Domain/homology
Chem-E0G / DNA sliding clamp PCNA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJossart, J.J. / Perry, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: Curr Res Struct Biol / Year: 2026
Title: Screening for novel chemical scaffolds targeting PCNA identifies the Hsp90alpha inhibitor SNX-2112.
Authors: Jossart, J. / Ma, N. / Haratipour, P. / Li, C.M. / Jang, C. / Gu, L. / O'Brien, T.E. / Vaidehi, N. / Malkas, L.H. / Hickey, R.J. / Perry, J.J.P.
History
DepositionJan 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2026Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4275
Polymers28,7961
Non-polymers6314
Water1,928107
1
A: Proliferating cell nuclear antigen
hetero molecules

A: Proliferating cell nuclear antigen
hetero molecules

A: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,28215
Polymers86,3873
Non-polymers1,89412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area5680 Å2
ΔGint-110 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.093, 141.093, 141.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA / Cyclin


Mass: 28795.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Chemical ChemComp-E0G / 4-[6,6-dimethyl-4-oxidanylidene-3-(trifluoromethyl)-5,7-dihydroindazol-1-yl]-2-[(4-oxidanylcyclohexyl)amino]benzamide


Mass: 464.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.18 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 0.2M sodium chloride, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→37.71 Å / Num. obs: 36913 / % possible obs: 99.97 % / Redundancy: 22.3 % / Biso Wilson estimate: 34.65 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06158 / Rpim(I) all: 0.01334 / Rrim(I) all: 0.06302 / Net I/σ(I): 34.49
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 22.8 % / Rmerge(I) obs: 1.417 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 3655 / CC1/2: 0.803 / CC star: 0.944 / Rpim(I) all: 0.3019 / Rrim(I) all: 1.449 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VKX

3vkx


Resolution: 1.9→37.71 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1999 5.42 %
Rwork0.2096 --
obs0.2109 36913 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 40 107 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081958
X-RAY DIFFRACTIONf_angle_d1.1182649
X-RAY DIFFRACTIONf_dihedral_angle_d7.106268
X-RAY DIFFRACTIONf_chiral_restr0.068310
X-RAY DIFFRACTIONf_plane_restr0.007333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30341400.27462456X-RAY DIFFRACTION100
1.95-20.25231380.232487X-RAY DIFFRACTION100
2-2.060.2771440.23612469X-RAY DIFFRACTION100
2.06-2.120.24611430.23132450X-RAY DIFFRACTION100
2.12-2.20.27411370.22672490X-RAY DIFFRACTION100
2.2-2.290.23671410.21942495X-RAY DIFFRACTION100
2.29-2.390.26531450.24112466X-RAY DIFFRACTION100
2.39-2.520.23181400.22742493X-RAY DIFFRACTION100
2.52-2.680.25551440.24422487X-RAY DIFFRACTION100
2.68-2.880.2641480.25122483X-RAY DIFFRACTION100
2.88-3.170.28881400.23382491X-RAY DIFFRACTION100
3.17-3.630.23141480.2022517X-RAY DIFFRACTION100
3.63-4.570.19251430.17322524X-RAY DIFFRACTION100
4.57-37.710.19991480.18632606X-RAY DIFFRACTION100

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