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- PDB-9ods: Structure of CRBN TBD bound to compound C3 -

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Basic information

Entry
Database: PDB / ID: 9ods
TitleStructure of CRBN TBD bound to compound C3
ComponentsProtein cereblon
KeywordsIMMUNE SYSTEM / Protein degrader
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination ...negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily
Similarity search - Domain/homology
: / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsStrickland, C. / Rice, C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Characterization of PVTX-321 as a Potent and Orally Bioavailable Estrogen Receptor Degrader for ER+/HER2- Breast Cancer.
Authors: Xu, G. / Havens, C.G. / Deng, Q. / Lowenstein, C. / Samanta, D. / Vidal, B. / Behshad, E. / Russell, M. / Orth, P. / Rice, C.T. / Nagilla, R. / Kirchhoff, P. / Chen, Z. / Rej, R.K. / ...Authors: Xu, G. / Havens, C.G. / Deng, Q. / Lowenstein, C. / Samanta, D. / Vidal, B. / Behshad, E. / Russell, M. / Orth, P. / Rice, C.T. / Nagilla, R. / Kirchhoff, P. / Chen, Z. / Rej, R.K. / Acharyya, R.K. / Wu, D. / Wang, S. / Zhang, W. / Wu, W. / Jolivette, L. / Strickland, C. / Sui, Z. / Mohammad, H.P. / Zhang, X. / Priestley, E.S.
History
DepositionApr 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
B: Protein cereblon
C: Protein cereblon
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,85512
Polymers49,2364
Non-polymers1,6198
Water55831
1
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7143
Polymers12,3091
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7143
Polymers12,3091
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7143
Polymers12,3091
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7143
Polymers12,3091
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.559, 86.279, 90.972
Angle α, β, γ (deg.)90.00, 114.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein cereblon


Mass: 12309.062 Da / Num. of mol.: 4 / Fragment: TBD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#2: Chemical
ChemComp-A1CAW / (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione


Mass: 339.349 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H17N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 0.2M tri-Sodium citrate 18 % w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.61→60.36 Å / Num. obs: 12509 / % possible obs: 62.6 % / Redundancy: 4.1 % / CC1/2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 2.61→2.85 Å / Num. unique obs: 3353 / CC1/2: 0.293

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
FFTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→60.36 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.896 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24802 614 4.9 %RANDOM
Rwork0.21484 ---
obs0.21642 11895 62.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20.28 Å2
2---0.91 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.61→60.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 104 31 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123609
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163265
X-RAY DIFFRACTIONr_angle_refined_deg1.021.8224935
X-RAY DIFFRACTIONr_angle_other_deg0.3361.7387575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.962548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69610569
X-RAY DIFFRACTIONr_chiral_restr0.0470.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
X-RAY DIFFRACTIONr_mcbond_it1.6586.6751732
X-RAY DIFFRACTIONr_mcbond_other1.6586.6751732
X-RAY DIFFRACTIONr_mcangle_it3.01511.9852158
X-RAY DIFFRACTIONr_mcangle_other3.01511.9872159
X-RAY DIFFRACTIONr_scbond_it1.3516.7081877
X-RAY DIFFRACTIONr_scbond_other1.3516.7081877
X-RAY DIFFRACTIONr_scangle_other2.51112.2742778
X-RAY DIFFRACTIONr_long_range_B_refined5.06762.013896
X-RAY DIFFRACTIONr_long_range_B_other5.06662.013897
LS refinement shellResolution: 2.61→2.674 Å
RfactorNum. reflection% reflection
Rfree0.307 3 -
Rwork0.357 54 -
obs--3.94 %

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