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- PDB-9y8m: Crystal structure of the Kelch domain of human KLHL12 with compound 8i -

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Basic information

Entry
Database: PDB / ID: 9y8m
TitleCrystal structure of the Kelch domain of human KLHL12 with compound 8i
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: 1.334 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)32,5512
Polymers32,1491
Non-polymers4021
Water6,557364
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)79.891, 79.891, 76.67
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-874-

HOH

21A-1006-

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-A1CTE / 2-(2-amino-5-fluoro-4-methyl-1H-1,3-benzimidazol-1-yl)-N-(2,4,6-trichlorophenyl)acetamide


Mass: 401.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12Cl3FN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 1.9 Å3/Da / Density % sol: 35.35 %
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: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.33→55.32 Å / Num. obs: 52105 / % possible obs: 91.4 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.8
Reflection shellResolution: 1.33→1.36 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 11.4 / Num. unique obs: 2758 / CC1/2: 0.988 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.334→45.521 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.34 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.057
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1785 2657 5.106 %
Rwork0.1635 49378 -
all0.164 --
obs-52035 91.378 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.126 Å20 Å20 Å2
2--0.126 Å20 Å2
3----0.253 Å2
Refinement stepCycle: LAST / Resolution: 1.334→45.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 25 364 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122300
X-RAY DIFFRACTIONr_angle_refined_deg2.071.8063157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9615309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.546516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29210352
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2731093
X-RAY DIFFRACTIONr_chiral_restr0.1270.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021794
X-RAY DIFFRACTIONr_nbd_refined0.2040.21073
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2820.262
X-RAY DIFFRACTIONr_mcbond_it1.2970.7331173
X-RAY DIFFRACTIONr_mcangle_it2.0981.3151471
X-RAY DIFFRACTIONr_scbond_it2.1040.9321127
X-RAY DIFFRACTIONr_scangle_it3.1761.6271673
X-RAY DIFFRACTIONr_lrange_it5.05711.74410714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.334-1.3690.1892020.16839410.16941430.980.9841000.159
1.369-1.4060.1831900.16438420.16540320.9790.9841000.156
1.406-1.4470.1731640.14936440.1539230.9820.98697.06860.143
1.447-1.4910.1851090.14923090.15138430.980.98662.91960.144
1.491-1.540.161430.15528850.15537150.9820.98581.50740.151
1.54-1.5940.1821710.14734090.14935800.980.9861000.146
1.594-1.6540.1751690.15232790.15334610.9810.98599.62440.152
1.654-1.7220.2011910.1631320.16333400.9760.98499.4910.163
1.722-1.7980.1751910.1630480.16132400.9810.98499.96910.166
1.798-1.8860.1721750.16128200.16230820.9820.98397.17720.169
1.886-1.9880.182720.16515070.16629330.9790.98453.83570.176
1.988-2.1080.1821200.1622870.16127770.980.98686.67630.17
2.108-2.2530.1721460.16223990.16326280.9840.98596.84170.174
2.253-2.4330.1561120.16720720.16724630.9840.98388.67230.184
2.433-2.6650.1911160.16421620.16622780.9760.9821000.185
2.665-2.9780.168970.1617710.16120680.9840.98490.32880.183
2.978-3.4360.1651140.1517180.15118320.9820.9861000.176
3.436-4.2020.145700.14412430.14415870.9880.98782.73470.174
4.202-5.9180.2670.18111900.18212570.9810.9831000.211
5.918-45.5210.298380.3237200.3227610.9770.96299.60580.35
Refinement TLS params.Method: refined / Origin x: -17.29 Å / Origin y: 14.5955 Å / Origin z: 0.3071 Å
111213212223313233
T0.0048 Å20.0014 Å20.0043 Å2-0.0008 Å2-0.0007 Å2--0.0164 Å2
L0.2161 °2-0.0318 °2-0.0515 °2-0.208 °20.0254 °2--0.0144 °2
S0.0152 Å °0.0071 Å °-0.004 Å °-0.0233 Å °-0.0115 Å °-0.0102 Å °-0.0063 Å °-0.0024 Å °-0.0037 Å °
Refinement TLS groupSelection: ALL

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