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- PDB-9sfm: Crystal structure of Cereblon-DDB1 in complex with SB-405483 and ... -

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Basic information

Entry
Database: PDB / ID: 9sfm
TitleCrystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide
Components
  • DNA damage-binding protein 1
  • Protein cereblon
KeywordsLIGASE / E3 ubiquitin ligase / substrate receptor / IMiDs (immunomodulatory drugs) / Allosteric modulator
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
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) / RSE1/DDB1/CPSF1 second beta-propeller ...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) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / S-Lenalidomide / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.39 Å
AuthorsChung, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: : Identification of an allosteric site on the E3 ligase adapter cereblon.
Authors: Chung, C.
History
DepositionAug 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,17611
Polymers172,1182
Non-polymers1,0579
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-11 kcal/mol
Surface area62600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.160, 129.518, 198.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 128139.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Strep tag / Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Protein Protein cereblon


Mass: 43978.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2

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Non-polymers , 5 types, 459 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LVY / S-Lenalidomide


Mass: 259.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O3
#6: Chemical ChemComp-A1CEG / N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea


Mass: 360.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N4O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.39→129.52 Å / Num. obs: 74800 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 16.6
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.228 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7356 / CC1/2: 0.828 / CC star: 0.952 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.39→99.4 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 3696 4.94 %RANDOM
Rwork0.1945 ---
obs0.197 74800 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→99.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11787 0 71 450 12308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912157
X-RAY DIFFRACTIONf_angle_d1.02216470
X-RAY DIFFRACTIONf_dihedral_angle_d6.6761635
X-RAY DIFFRACTIONf_chiral_restr0.0591869
X-RAY DIFFRACTIONf_plane_restr0.012116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.420.31921250.25862603X-RAY DIFFRACTION96
2.42-2.450.28981450.2412696X-RAY DIFFRACTION100
2.45-2.490.29981320.24142746X-RAY DIFFRACTION100
2.49-2.520.30191530.24922660X-RAY DIFFRACTION100
2.52-2.560.41221430.33692672X-RAY DIFFRACTION100
2.56-2.60.37131210.34812761X-RAY DIFFRACTION100
2.6-2.650.37871560.33322697X-RAY DIFFRACTION100
2.65-2.70.38571450.29452728X-RAY DIFFRACTION100
2.7-2.750.33491460.27122683X-RAY DIFFRACTION100
2.75-2.810.30821340.23082704X-RAY DIFFRACTION100
2.81-2.870.29071350.2132725X-RAY DIFFRACTION100
2.87-2.930.27971480.21622700X-RAY DIFFRACTION100
2.93-3.010.2861570.21882724X-RAY DIFFRACTION100
3.01-3.090.26951630.23742694X-RAY DIFFRACTION100
3.09-3.180.27931430.24622705X-RAY DIFFRACTION100
3.18-3.280.28381500.23362738X-RAY DIFFRACTION100
3.28-3.40.2581450.19632723X-RAY DIFFRACTION100
3.4-3.540.23981310.18692736X-RAY DIFFRACTION100
3.54-3.70.26211380.17652740X-RAY DIFFRACTION100
3.7-3.890.20731350.17682769X-RAY DIFFRACTION100
3.89-4.140.22341190.1692771X-RAY DIFFRACTION100
4.14-4.450.19651510.15022756X-RAY DIFFRACTION100
4.45-4.90.19271660.13912742X-RAY DIFFRACTION100
4.9-5.610.24211370.16442812X-RAY DIFFRACTION100
5.61-7.070.21791450.18542835X-RAY DIFFRACTION100
7.07-99.40.1831330.17692984X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.1612 Å / Origin y: 23.2334 Å / Origin z: -53.5681 Å
111213212223313233
T0.2802 Å2-0.0179 Å20.0276 Å2-0.285 Å20.0235 Å2--0.3059 Å2
L0.1776 °2-0.0664 °20.0407 °2-0.2817 °2-0.1953 °2--0.2964 °2
S-0.0086 Å °0.0139 Å °0.0247 Å °-0.0246 Å °-0.0151 Å °-0.0136 Å °-0.0303 Å °-0.0339 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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