9jk1

Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin-dependent kinase 12

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cyclin-K × 1 （O75909） 1,2-ETHANEDIOL × 2 ;N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide ; × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cyclin-K × 1 （O75909） ;N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide ; × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDK12_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–340； UniProt 715–1052 Author chain B； PDBConstruct 3–340； UniProt 715–1052

Cyclin-K

Homo sapiens

UniProt O75909

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cyclin-dependent kinase 12 × 1 （Q9NYV4） 1,2-ETHANEDIOL × 2 ;N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide ; × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cyclin-dependent kinase 12 × 1 （Q9NYV4） ;N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide ; × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–269； UniProt 1–267 Author chain D； PDBConstruct 3–269； UniProt 1–267

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9jk1
Deposition date deposition_date	2024-09-14
Last revision last_revision	2025-05-07
Structure title title	Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118
Keywords keywords	kinase, covalent inhibitor, selective, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9jk1__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9jk1__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9jk1__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.27 Å
Rg (electron density)	27.25 Å
Total Rg	27.99 Å
Atom count	4327
Residues	549
Excluded volume	77319 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9jk1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9jk1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent kinase 12
Molecular weight formula_weight	39629.8 kDa
EC 编号 ec_number	2.7.11.22,2.7.11.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8709

GATESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQRQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cyclin-K
Molecular weight formula_weight	31500.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

GAMKENKENSSPSVTSANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide ;
Molecular weight formula_weight	622.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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Unit-cell length a length_a	50.200 Å
Unit-cell length b length_b	77.190 Å
Unit-cell length c length_c	91.460 Å
Unit-cell angle α angle_alpha	75.88 °
Unit-cell angle β angle_beta	85.63 °
Unit-cell angle γ angle_gamma	77.92 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	29.560 Å
R factor r_factor	0.2493
R_work r_work	0.2482
R_free r_free	0.2665

Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin-dependent kinase 12

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-K

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9jk1__assembly_2__model_1

9jk1__assembly_2__model_1 | I(q)

9jk1__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin-dependent kinase 12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cyclin-K

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9jk1__assembly_2__model_1

9jk1__assembly_2__model_1 | I(q)

9jk1__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)