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- PDB-9y8u: Crystal structure of the Kelch domain of human KLHL12 with compou... -

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Basic information

Entry
Database: PDB / ID: 9y8u
TitleCrystal structure of the Kelch domain of human KLHL12 with compound 10j
ComponentsKelch-like protein 12
KeywordsLIGASE / E3 ligase / fragment-based drug discovery / PROTAC
Function / homology
Function and homology information


neural crest formation / neural crest cell development / COPII vesicle coat assembly / COPII vesicle coat / COPII-coated ER to Golgi transport vesicle / Cul3-RING ubiquitin ligase complex / endoplasmic reticulum to Golgi vesicle-mediated transport / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / Degradation of DVL ...neural crest formation / neural crest cell development / COPII vesicle coat assembly / COPII vesicle coat / COPII-coated ER to Golgi transport vesicle / Cul3-RING ubiquitin ligase complex / endoplasmic reticulum to Golgi vesicle-mediated transport / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / Degradation of DVL / Wnt signaling pathway / centriolar satellite / proteasome-mediated ubiquitin-dependent protein catabolic process / identical protein binding / cytoplasm / cytosol
Similarity search - Function
KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain ...KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
: / Kelch-like protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsAmporndanai, K. / Madrigal-Carrillo, E.A. / Rietz, T.A. / Zhao, B. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Identification of KLHL12 Ligands Using Fragment-Based Methods.
Authors: Waterson, A.G. / Vadukoot, A. / Jana, S. / Cui, J. / Luong, K. / Rietz, T.A. / Madrigal-Carrillo, E.A. / Lehmann, B.D. / Sensintaffar, J.L. / Zhao, B. / Amporndanai, K. / Petros, Z.A. / ...Authors: Waterson, A.G. / Vadukoot, A. / Jana, S. / Cui, J. / Luong, K. / Rietz, T.A. / Madrigal-Carrillo, E.A. / Lehmann, B.D. / Sensintaffar, J.L. / Zhao, B. / Amporndanai, K. / Petros, Z.A. / Scaggs, W.R. / Chacon Simon, S. / Vekariya, R.H. / Kim, K. / Thangaraj, M. / Christov, P.P. / South, T.M. / Sai, J. / Thiruvaipati, A. / Schmidt, C.R. / Eells, R. / Moore, W.J. / Olejniczak, E.T. / Phan, J. / Fesik, S.W.
History
DepositionSep 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7092
Polymers32,1491
Non-polymers5601
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.040, 80.040, 77.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-910-

HOH

21A-1015-

HOH

31A-1058-

HOH

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Components

#1: Protein Kelch-like protein 12 / CUL3-interacting protein 1 / DKIR homolog / hDKIR


Mass: 32148.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL12, C3IP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53G59
#2: Chemical ChemComp-A1CTK / 2-(4-{[(3S)-3-(4-cyanopiperidin-1-yl)pyrrolidin-1-yl]methyl}-2-methyl-1H-1,3-benzimidazol-1-yl)-N-(2,4,6-trichlorophenyl)acetamide


Mass: 559.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29Cl3N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 1.92 Å3/Da / Density % sol: 36.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 5.5, 0.2M MgCl2 and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.01→56.6 Å / Num. obs: 120772 / % possible obs: 92.8 % / Redundancy: 1.9 % / CC1/2: 1 / Rmerge(I) obs: 0.01 / Rpim(I) all: 0.01 / Rrim(I) all: 0.015 / Χ2: 0.87 / Net I/σ(I): 37.6 / Num. measured all: 226788
Reflection shellResolution: 1.01→1.03 Å / % possible obs: 42.9 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.306 / Num. measured all: 3409 / Num. unique obs: 2713 / CC1/2: 0.758 / Rpim(I) all: 0.306 / Rrim(I) all: 0.432 / Χ2: 0.52 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→56.6 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.529 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.14108 6106 5.1 %RANDOM
Rwork0.12524 ---
obs0.12603 114666 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.01→56.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 37 384 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122331
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162130
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.8163191
X-RAY DIFFRACTIONr_angle_other_deg0.7421.7554896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8235305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.495518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21310361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
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_it3.6220.9561171
X-RAY DIFFRACTIONr_mcbond_other3.6070.9561171
X-RAY DIFFRACTIONr_mcangle_it5.261.7271467
X-RAY DIFFRACTIONr_mcangle_other5.2641.731468
X-RAY DIFFRACTIONr_scbond_it5.3071.1931160
X-RAY DIFFRACTIONr_scbond_other5.3041.1931161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5192.11715
X-RAY DIFFRACTIONr_long_range_B_refined12.91113.812751
X-RAY DIFFRACTIONr_long_range_B_other11.18911.292604
X-RAY DIFFRACTIONr_rigid_bond_restr4.29334461
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.012→1.038 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 236 -
Rwork0.295 4380 -
obs--48.38 %

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