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- PDB-9htn: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 9htn
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2s
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / CEREBLON / Ubiquitination / E3 / MOLECULAR GLUE
Function / homologyCULT domain / CULT domain profile. / metal ion binding / : / : / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsBischof, L. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Extending the chemical space of glutarimide-based cereblon ligands through an efficient Rh(II)-catalyzed X-H insertion reaction.
Authors: Levashova, E. / Bischof, L. / Bunev, A. / Sapegin, A. / Grygor'eva, O. / Kudinov, A. / Ebeling, S. / Tatarinov, I. / Dar'in, D. / Kantin, G. / Hartmann, M.D. / Kalinin, S.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 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: Cereblon isoform 4
B: Cereblon isoform 4
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,13510
Polymers41,1113
Non-polymers1,0247
Water99155
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1084
Polymers13,7041
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0133
Polymers13,7041
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0133
Polymers13,7041
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.470, 60.042, 88.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cereblon isoform 4


Mass: 13703.577 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4TVL0

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Non-polymers , 5 types, 62 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1IW7 / (3R)-3-(3,4-dihydro-2H-quinolin-1-yl)piperidine-2,6-dione


Mass: 244.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-A1I4Q / (3S)-3-(3,4-dihydro-2H-quinolin-1-yl)piperidine-2,6-dione


Mass: 244.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.8 Å3/Da / Density % sol: 31.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.92→19.69 Å / Num. obs: 22809 / % possible obs: 96.4 % / Redundancy: 12.56 % / Biso Wilson estimate: 44.089 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.3
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 13.33 % / Mean I/σ(I) obs: 1.22 / Num. unique obs: 2900 / CC1/2: 0.526 / % possible all: 77.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.92→19.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.689 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23532 1140 5 %RANDOM
Rwork0.19051 ---
obs0.19272 21669 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å20 Å2
2---0.3 Å2-0 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.92→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 62 55 2486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172253
X-RAY DIFFRACTIONr_angle_refined_deg1.741.6433505
X-RAY DIFFRACTIONr_angle_other_deg1.631.5725156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2125317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77319.695131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58715337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5211520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5272.4351256
X-RAY DIFFRACTIONr_mcbond_other1.5272.4341255
X-RAY DIFFRACTIONr_mcangle_it2.4553.6321568
X-RAY DIFFRACTIONr_mcangle_other2.4543.6321569
X-RAY DIFFRACTIONr_scbond_it1.9562.6471320
X-RAY DIFFRACTIONr_scbond_other1.8832.6411317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9633.8951929
X-RAY DIFFRACTIONr_long_range_B_refined4.69826.962702
X-RAY DIFFRACTIONr_long_range_B_other4.68826.892699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A28560.14
12B28560.14
21A27750.13
22C27750.13
31B27410.13
32C27410.13
LS refinement shellResolution: 1.92→1.967 Å
RfactorNum. reflection% reflection
Rfree0.313 44 -
Rwork0.309 870 -
obs--52.56 %
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)
12.89460.01410.68091.9972.14694.68870.03080.0651-0.16990.050.00910.05230.20450.015-0.03990.01110.003-0.00330.0317-0.00910.12919.425318.49152.3054
23.6723-1.27270.59832.7876-0.66582.46660.01150.0076-0.1049-0.0488-0.01320.02560.01920.05450.00170.0041-0.00710.00610.03770.02280.087932.19668.085423.9989
32.62281.5776-0.12245.2579-0.25132.0571-0.01610.0341-0.0307-0.23490.01590.37730.2241-0.36870.00020.1276-0.0190.01370.24020.00080.233928.1684-6.5716-6.8407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 151
2X-RAY DIFFRACTION2B19 - 151
3X-RAY DIFFRACTION3C17 - 201

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