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- PDB-9y8j: Crystal structure of the Kelch domain of human KLHL12 with compound 1 -

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Basic information

Entry
Database: PDB / ID: 9y8j
TitleCrystal structure of the Kelch domain of human KLHL12 with compound 1
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: 2.7 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)32,4182
Polymers32,1491
Non-polymers2691
Water00
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)135.258, 135.258, 71.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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-A1CTS / 2-(1H-1,3-benzimidazol-1-yl)-N-(2-fluorophenyl)acetamide


Mass: 269.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12FN3O / Feature type: SUBJECT OF INVESTIGATION
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: 1.97 Å3/Da / Density % sol: 37.6 %
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-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.7→29.613 Å / Num. obs: 7049 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 624 / CC1/2: 0.369

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.613 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 39.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3291 705 10 %
Rwork0.2931 --
obs0.2969 7049 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 20 0 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072133
X-RAY DIFFRACTIONf_angle_d0.9522916
X-RAY DIFFRACTIONf_dihedral_angle_d16.412705
X-RAY DIFFRACTIONf_chiral_restr0.055331
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.90840.43241380.4091244X-RAY DIFFRACTION100
2.9084-3.20080.47921390.38551254X-RAY DIFFRACTION100
3.2008-3.66320.38431410.34441271X-RAY DIFFRACTION100
3.6632-4.61250.2981410.26071266X-RAY DIFFRACTION100
4.6125-29.6130.25821460.23841309X-RAY DIFFRACTION100
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)
11.69880.3708-0.7993.7771-1.13362.4963-0.11380.7690.6938-1.0964-0.0118-0.31390.33510.38240.12120.5057-0.0198-0.04520.78190.34130.58469.432620.266492.0404
20.9924-0.76750.3162.0455-0.25021.7101-0.25520.48010.9459-0.15980.08750.2433-0.06310.25060.11450.3539-0.081-0.25770.50840.18930.6959-1.006522.683102.4618
30.3311-0.3050.05750.5015-0.45021.0458-0.18290.18320.5323-0.3063-0.03720.3779-0.0939-0.3980.12460.6601-0.1606-0.44980.90120.24350.9078-15.512825.274993.3066
40.5739-1.14820.5912.5702-1.96372.9269-0.08150.10490.2352-0.16980.07110.2001-0.0816-0.1931-0.00781.0959-0.236-0.51230.96030.46271.0811-9.69726.626982.071
50.0081-0.0070.06570.0062-0.06080.559-0.08950.24410.2026-0.3129-0.01030.1146-0.0661-0.0926-0.06171.2602-0.1925-0.43521.54250.44520.7625-6.075223.456379.102
61.4728-0.03530.08560.4611-0.09080.7019-0.13090.66130.4049-0.7997-0.3133-0.18450.02140.13950.44231.0539-0.2028-0.12011.32810.31350.46975.114721.032380.6533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 280 through 334 )
2X-RAY DIFFRACTION2chain 'A' and (resid 335 through 408 )
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 456 )
4X-RAY DIFFRACTION4chain 'A' and (resid 457 through 478 )
5X-RAY DIFFRACTION5chain 'A' and (resid 479 through 525 )
6X-RAY DIFFRACTION6chain 'A' and (resid 526 through 567 )

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