PDB-9y8v: Crystal structure of the Kelch domain of human KLHL12 with compou...

ID or keywords:

Entry

Database: PDB / ID: 9y8v

Title

Crystal structure of the Kelch domain of human KLHL12 with compound 10q

Components

Kelch-like protein 12

Keywords

LIGASE / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.271 Å

Authors

Amporndanai, K. / Madrigal-Carrillo, E.A. / Rietz, T.A. / Zhao, B. / Fesik, S.W.

Funding support

United States, 1items

Citation

Journal: 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. / ...

History

Deposition	Sep 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2026	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2026	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9y8v.cif.gz	293.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y8/9y8v ftp://data.pdbj.org/pub/pdb/validation_reports/y8/9y8v	HTTPS FTP

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Related structure data

Related structure data	9y8jC 9y8kC 9y8lC 9y8mC 9y8nC 9y8oC 9y8qC 9y8rC 9y8sC 9y8tC 9y8uC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (2) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Kelch-like protein 12

hetero molecules

32.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.571, 79.571, 76.631
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-819- HOH
2	1	A-838- HOH
3	1	A-942- HOH

#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-A1CTF / 2-{4-[(1R,2S)-2-{[(3S)-3-(1,1-dioxo-1lambda~6~-thiomorpholin-4-yl)pyrrolidin-1-yl]methyl}cyclopropyl]-2-methyl-1H-1,3-benzimidazol-1-yl}-N-(2,4,6-trichlorophenyl)acetamide Mass: 625.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₈H₃₂Cl₃N₅O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 34.8 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2023
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.271→56.329 Å / Num. obs: 59437 / % possible obs: 96.4 % / Redundancy: 10.7 % / CC_1/2: 1 / R_merge(I) obs: 0.051 / Net I/σ(I): 25.2
Reflection shell	Resolution: 1.271→1.38 Å / Redundancy: 1.7 % / R_merge(I) obs: 1.06 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1291 / CC_1/2: 0.404 / % possible all: 50.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
MOSFLM		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.271→56.329 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.966 / SU B: 3.32 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1994	2836	4.771 %
R_work	0.1604	56601	-
all	0.162	-	-
obs	-	59437	91.234 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 12.324 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.261 Å²	0 Å²	0 Å²
2-	-	1.261 Å²	0 Å²
3-	-	-	-2.523 Å²

Refinement step

Cycle: LAST / Resolution: 1.271→56.329 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2166	0	40	274	2480

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2322
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2115
X-RAY DIFFRACTION	r_angle_refined_deg	1.7	1.816	3191
X-RAY DIFFRACTION	r_angle_other_deg	0.641	1.747	4866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.838	5	309
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.815	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.551	10	353
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.917	10	94
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	359
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2811
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	542
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	438
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	2203
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1156
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	1269
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.214	0.2	215
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.267	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.274	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.23	0.2	63
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.22	0.2	32
X-RAY DIFFRACTION	r_mcbond_it	2.954	1.018	1173
X-RAY DIFFRACTION	r_mcbond_other	2.951	1.018	1173
X-RAY DIFFRACTION	r_mcangle_it	4.579	1.825	1471
X-RAY DIFFRACTION	r_mcangle_other	4.581	1.826	1472
X-RAY DIFFRACTION	r_scbond_it	3.833	1.204	1149
X-RAY DIFFRACTION	r_scbond_other	3.823	1.203	1148
X-RAY DIFFRACTION	r_scangle_it	5.694	2.139	1704
X-RAY DIFFRACTION	r_scangle_other	5.692	2.139	1705
X-RAY DIFFRACTION	r_lrange_it	10.9	14.415	10823
X-RAY DIFFRACTION	r_lrange_other	9.54	13.574	10514
X-RAY DIFFRACTION	r_rigid_bond_restr	3.523	3	4437

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.271-1.304	0.408	82	0.391	2005	0.392	4755	0.638	0.698	43.8906	0.396
1.304-1.34	0.383	143	0.361	2931	0.362	4609	0.883	0.905	66.6956	0.364
1.34-1.378	0.349	199	0.339	3433	0.34	4502	0.893	0.915	80.6753	0.34
1.378-1.421	0.332	216	0.31	3743	0.311	4388	0.924	0.937	90.2233	0.312
1.421-1.467	0.287	239	0.283	3842	0.283	4247	0.953	0.952	96.0914	0.282
1.467-1.519	0.259	162	0.237	3898	0.238	4097	0.964	0.969	99.0969	0.235
1.519-1.576	0.185	166	0.18	3819	0.18	3985	0.983	0.984	100	0.17
1.576-1.641	0.215	198	0.162	3633	0.164	3831	0.974	0.987	100	0.146
1.641-1.713	0.185	201	0.149	3473	0.151	3674	0.982	0.989	100	0.128
1.713-1.797	0.225	142	0.14	3385	0.143	3527	0.973	0.989	100	0.113
1.797-1.894	0.201	141	0.131	3237	0.134	3378	0.976	0.991	100	0.108
1.894-2.009	0.184	171	0.126	3017	0.128	3188	0.98	0.992	100	0.107
2.009-2.147	0.162	150	0.126	2833	0.128	2983	0.988	0.993	100	0.112
2.147-2.319	0.158	138	0.123	2672	0.125	2810	0.987	0.993	100	0.108
2.319-2.54	0.167	123	0.126	2468	0.128	2591	0.984	0.991	100	0.106
2.54-2.839	0.172	111	0.129	2273	0.131	2384	0.981	0.99	100	0.112
2.839-3.277	0.154	87	0.137	2005	0.138	2092	0.986	0.988	100	0.123
3.277-4.01	0.149	68	0.124	1742	0.125	1810	0.987	0.991	100	0.118
4.01-5.657	0.188	62	0.143	1365	0.145	1427	0.985	0.991	100	0.143
5.657-56.329	0.335	37	0.262	826	0.265	863	0.947	0.967	100	0.261

Refinement TLS params.

Method: refined / Origin x: -14.5076 Å / Origin y: -17.2139 Å / Origin z: -18.7841 Å

	11	12	13	21	22	23	31	32	33
T	0.0028 Å²	0.0008 Å²	-0.0012 Å²	-	0.0152 Å²	0.0045 Å²	-	-	0.0578 Å²
L	1.167 °²	0.3252 °²	-0.1866 °²	-	1.4917 °²	-0.0958 °²	-	-	0.1065 °²
S	-0.0052 Å °	0.0932 Å °	0.0077 Å °	-0.0611 Å °	0.028 Å °	0.0236 Å °	-0.0011 Å °	-0.0389 Å °	-0.0228 Å °

Refinement TLS group

Selection: ALL

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