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4f6u

Crystal structure of human CDK8/CYCC in complex with compound 5 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea)

Method: X-RAY DIFFRACTION Dmax: 89.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclin-dependent kinase 8

Homo sapiens

UniProt P49336

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–403 Fragment：UNP residues 1-403 Cyclin-C × 1 （P24863） 0SR 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea × 1 NA SODIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 10 FMT FORMIC ACID × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K Resolution 2.10 Å R-free 0.198

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4F6U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RGF Crystal Structure of human CDK8/CycC Deposited 2011-04-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded BAX 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE × 1 EDO 1,2-ETHANEDIOL × 11 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.221
4CRL Crystal structure of human CDK8-Cyclin C in complex with cortistatin A Deposited 2014-02-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：KINASE DOMAIN, RESIDUES 1-403
Not recorded C1I CORTISTATIN A × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M LITHIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Resolution 2.40 Å R-free 0.256
4F6S Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea) Deposited 2012-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0SQ 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea × 1 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.60 Å R-free 0.260
4F6W Crystal structure of human CDK8/CYCC in complex with compound 1 (N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide) Deposited 2012-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0SS N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 9 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.39 Å R-free 0.234
4F70 Crystal structure of human CDK8/CYCC in complex with compound 4 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[2-(morpholin-4-yl)ethyl]urea) Deposited 2012-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0ST 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[2-(morpholin-4-yl)ethyl]urea × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.239
4F7J Crystal structure of human CDK8/CYCC in complex with compound 3 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(2-hydroxyethyl)urea) Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0SU 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(2-hydroxyethyl)urea × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.60 Å R-free 0.276
4F7L Crystal structure of human CDK8/CYCC in complex with compound 2 (tert-butyl [3-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)propyl]carbamate) Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0SO tert-butyl [3-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)propyl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.90 Å R-free 0.270
4F7N Crystal structure of human CDK8/CYCC in complex with compound 11 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)urea) Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0SV 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)urea × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.65 Å R-free 0.228
4F7S Crystal structure of human CDK8/CYCC in the DMG-in conformation Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 0SW N-(2-phenylethyl)quinazolin-4-amine × 1 EDO 1,2-ETHANEDIOL × 13 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.20 Å R-free 0.222
4G6L Crystal structure of human CDK8/CYCC in the DMG-in conformation Deposited 2012-07-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.266
5BNJ CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-phenyl]-pyridin- 4-yl}-2,8-diaza-spiro[4.5]decan-1-one Deposited 2015-05-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：KINASE DOMAIN, residues 3-405
Not recorded 4TV 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；293 K；20% PEG3350, 0.2 M sodium formate, pH 6.9,
Resolution 2.64 Å R-free 0.273
5CEI Crystal structure of CDK8:Cyclin C complex with compound 22 Deposited 2015-07-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded EDO 1,2-ETHANEDIOL × 8 FMT FORMIC ACID × 7 50R 4-(4-iodophenoxy)-N-methylthieno[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350 and 0.20 M sodium formate
Resolution 2.24 Å R-free 0.227
5FGK CDK8-CYCC IN COMPLEX WITH 8-[3-(3-Amino-1H-indazol-6-yl)-5-chloro- pyridine-4-yl]-2,8-diaza-spiro[4.5]decan-1-one Deposited 2015-12-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-405
Not recorded 5XG 8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2 FMT FORMIC ACID × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 0；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 2.36 Å R-free 0.237
5HBE CDK8-CYCC IN COMPLEX WITH 8-[3-Chloro-5-(1-methyl-2,2-dioxo-2, 3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-pyridin- 4-yl]-1-oxa-3,8-diaza-spiro[4.5]decan-2-one Deposited 2015-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 1-362
Not recorded 5Y6 8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 2.38 Å R-free 0.256
5HBH CDK8-CYCC IN COMPLEX WITH 5-{5-Chloro-4-[1-(2-methoxy-ethyl)-1,8-diaza-spiro[4.5]dec-8-yl]-pyridin-3-yl}-1-methyl-1,3-dihydro-benzo[c]isothiazole 2,2-dioxide Deposited 2015-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 1-362
Not recorded 5Y7 5-[5-chloranyl-4-[1-(2-methoxyethyl)-1,8-diazaspiro[4.5]decan-8-yl]pyridin-3-yl]-1-methyl-3~{H}-2,1-benzothiazole 2,2-dioxide × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 2.50 Å R-free 0.268
5HBJ CDK8-CYCC IN COMPLEX WITH 8-[2-Amino-3-chloro-5-(1-methyl-1H-indazol-5-yl)-pyridin-4-yl]-2,8-diaza-spiro[4.5]decan-1-one Deposited 2015-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-362
Not recorded 5Y8 8-[2-azanyl-3-chloranyl-5-(1-methylindazol-5-yl)pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 3.00 Å R-free 0.288
5HNB CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone Deposited 2016-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 1-362
Not recorded 62M [6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone × 1 FMT FORMIC ACID × 6 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M lithium chloride
Resolution 2.35 Å R-free 0.252
5HVY CDK8/CYCC IN COMPLEX WITH COMPOUND 20 Deposited 2016-01-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa） Fragment：UNP residues 1-403
Not recorded 66X N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea × 1 FMT FORMIC ACID × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG 3350 and 0.20 M sodium formate
Resolution 2.39 Å R-free 0.220
5I5Z CDK8-CYCC IN COMPLEX WITH 8-(1-Methyl-2,2-dioxo-2,3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-[1,6]naphthyridine-2-carboxylic acid methylamide Deposited 2016-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 3-405
Not recorded 68U N-methyl-8-(1-methyl-2,2-dioxo-2,3-dihydro-1H-2lambda~6~,1-benzothiazol-5-yl)-1,6-naphthyridine-2-carboxamide × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG3350, 0.2 M sodium formate, pH 6.9
Resolution 2.60 Å R-free 0.274
5ICP CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(5-methyl-imidazo[5,1-b][1,3,4]thiadiazol-2-yl)-methanone Deposited 2016-02-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa） Fragment：KINASE DOMAIN, RESIDUES 1-362
Not recorded 69Z [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](5-methylimidazo[5,1-b][1,3,4]thiadiazol-2-yl)methanone × 1 EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG3350, 0.2 M sodium formate, pH 6.9
Resolution 2.18 Å R-free 0.216
5IDN CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-methanone Deposited 2016-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–364（364 aa） Fragment：KINASE DOMAIN, RESIDUES 3-405
Not recorded 6A7 [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG 3350, 0.2 M sodium formate, pH 6.9
Resolution 2.26 Å R-free 0.253
5IDP CDK8-CYCC IN COMPLEX WITH (3-Amino-1H-indazol-5-yl)-[(S)-2-(4-fluoro-phenyl)-piperidin-1-yl]-methanone Deposited 2016-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–364（364 aa） Fragment：KINASE DOMAIN, RESIDUES 3-405
Not recorded 6A6 (3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG 3350, 0.2 M sodium formate, pH 6.9
Resolution 2.65 Å R-free 0.272
5XQX Human CDK8-CYCC in complex with compound 4: N-methyl-4-(4-pyridyl)-1H-pyrrole-2-carboxamide Deposited 2017-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–371（371 aa） Fragment：UNP residues 1-371
Not recorded GOL GLYCEROL × 2 8CC N-methyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05M MgCl, 0.1M MES pH 6.5, 10% Iso-propanol, 5% PEG4K
Resolution 2.30 Å R-free 0.222
5XS2 CDK8-CYCC IN COMPLEX WITH COMPOUND 17:3-chloro-4-(4-pyridyl)-1H-pyrrole-2-carboxamide Deposited 2017-06-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–371（371 aa） Fragment：UNP residues 1-371
Not recorded GOL GLYCEROL × 1 8D6 3-chloranyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05M MgCl, 0.1M MES pH 6.5, 10% Iso-propanol, 5% PEG4K
Resolution 2.04 Å R-free 0.225
6QTG Crystal structure of human CDK8/CYCC in complex with BI-1347 Deposited 2019-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded JH8 2-[4-(4-isoquinolin-4-ylphenyl)pyrazol-1-yl]-~{N},~{N}-dimethyl-ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；32-38% Morpheus Precipitant Mix 4 10 mmol/L Morpheus Buffer System 1 100 mM Morpheus Amino Acids Mix 2% DMSO
Resolution 2.70 Å R-free 0.231
6QTJ Crystal structure of human CDK8/CYCC in complex with BI 919811 Deposited 2019-02-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded JHK ~{N},~{N}-dimethyl-2-[4-[4-(2,6-naphthyridin-4-yl)phenyl]pyrazol-1-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；32-38% Morpheus Precipitant Mix 4 10 mmol/L Morpheus Buffer System 1 100 mM Morpheus Amino Acids Mix 2% DMSO
Resolution 2.48 Å R-free 0.220
6R3S CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH COMPOUND 1 Deposited 2019-03-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded JRE 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.19 Å R-free 0.227
6T41 CDK8/Cyclin C in complex with N-(4-chlorobenzyl)isoquinolin-4-amine Deposited 2019-10-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–404（404 aa）
Not recorded MFE ~{N}-[(4-chlorophenyl)methyl]quinazolin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20%(w/v) PEG-3350 and 0.2 M sodium formate
Resolution 2.45 Å R-free 0.256
6TPA CDK8/CyclinC in complex with drug ETP-50775 Deposited 2019-12-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded NZ8 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-(5-oxidanylidene-6-pyridin-4-yl-pyrido[2,3-b][1,5]benzoxazepin-9-yl)urea × 1 FMT FORMIC ACID × 12 NZ5 (2~{R})-butane-1,2-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 3350, 200mM NaFormate, 3% Butanediol
Resolution 2.80 Å R-free 0.264
6Y0A CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH BI00690300 Deposited 2020-02-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded JRE 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；20% (wt/vol) polyethylene glycol 3350 0.2 M sodium formate
Resolution 2.19 Å R-free 0.227
8TQ2 Structure of the kinase lobe of human CDK8 kinase module Deposited 2023-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–464（464 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TQC Structure of the human CDK8 kinase module Deposited 2023-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–464（464 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TQW Structure of human transcriptional Mediator complex Deposited 2023-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain a 1–464（464 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
9H8C Human CDK8/Cyclin-C complex with inhibitor 2-9 Deposited 2024-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 A1IS8 4-[(3~{S})-3-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]piperidin-1-yl]carbonyl-1~{H}-pyrrole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES pH6.5, HEPES pH6.8, Sodium Formate
Resolution 2.57 Å R-free 0.262
9H8S Human CDK8/Cyclin-C complex with inhibitor 3-7 Deposited 2024-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–403（403 aa）
Not recorded CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1 A1ITF 4-[(3~{S},5~{R})-3-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]-5-methoxy-piperidin-1-yl]carbonyl-1~{H}-pyrrole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES pH6.5, HEPES pH6.8, Sodium Formate
Resolution 2.16 Å R-free 0.248

35 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDK8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–405； UniProt 1–403

Cyclin-C

Homo sapiens

UniProt P24863

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–283 Not recorded Cyclin-dependent kinase 8 × 1 （P49336） 0SR 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea × 1 NA SODIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 10 FMT FORMIC ACID × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K Resolution 2.10 Å R-free 0.198

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4F6U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RGF Crystal Structure of human CDK8/CycC Deposited 2011-04-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded BAX 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE × 1 EDO 1,2-ETHANEDIOL × 11 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.221
4CRL Crystal structure of human CDK8-Cyclin C in complex with cortistatin A Deposited 2014-02-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded C1I CORTISTATIN A × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M LITHIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Resolution 2.40 Å R-free 0.256
4F6S Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea) Deposited 2012-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0SQ 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea × 1 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.60 Å R-free 0.260
4F6W Crystal structure of human CDK8/CYCC in complex with compound 1 (N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide) Deposited 2012-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0SS N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 9 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.39 Å R-free 0.234
4F70 Crystal structure of human CDK8/CYCC in complex with compound 4 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[2-(morpholin-4-yl)ethyl]urea) Deposited 2012-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0ST 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[2-(morpholin-4-yl)ethyl]urea × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 3.00 Å R-free 0.239
4F7J Crystal structure of human CDK8/CYCC in complex with compound 3 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(2-hydroxyethyl)urea) Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0SU 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(2-hydroxyethyl)urea × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.60 Å R-free 0.276
4F7L Crystal structure of human CDK8/CYCC in complex with compound 2 (tert-butyl [3-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)propyl]carbamate) Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0SO tert-butyl [3-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)propyl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.90 Å R-free 0.270
4F7N Crystal structure of human CDK8/CYCC in complex with compound 11 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)urea) Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0SV 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-(5-hydroxypentyl)urea × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.65 Å R-free 0.228
4F7S Crystal structure of human CDK8/CYCC in the DMG-in conformation Deposited 2012-05-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 0SW N-(2-phenylethyl)quinazolin-4-amine × 1 EDO 1,2-ETHANEDIOL × 13 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.20 Å R-free 0.222
4G6L Crystal structure of human CDK8/CYCC in the DMG-in conformation Deposited 2012-07-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.70 Å R-free 0.266
5BNJ CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-phenyl]-pyridin- 4-yl}-2,8-diaza-spiro[4.5]decan-1-one Deposited 2015-05-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 4TV 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；293 K；20% PEG3350, 0.2 M sodium formate, pH 6.9,
Resolution 2.64 Å R-free 0.273
5CEI Crystal structure of CDK8:Cyclin C complex with compound 22 Deposited 2015-07-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded EDO 1,2-ETHANEDIOL × 8 FMT FORMIC ACID × 7 50R 4-(4-iodophenoxy)-N-methylthieno[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350 and 0.20 M sodium formate
Resolution 2.24 Å R-free 0.227
5FGK CDK8-CYCC IN COMPLEX WITH 8-[3-(3-Amino-1H-indazol-6-yl)-5-chloro- pyridine-4-yl]-2,8-diaza-spiro[4.5]decan-1-one Deposited 2015-12-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 5XG 8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2 FMT FORMIC ACID × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 0；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 2.36 Å R-free 0.237
5HBE CDK8-CYCC IN COMPLEX WITH 8-[3-Chloro-5-(1-methyl-2,2-dioxo-2, 3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-pyridin- 4-yl]-1-oxa-3,8-diaza-spiro[4.5]decan-2-one Deposited 2015-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 5Y6 8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 2.38 Å R-free 0.256
5HBH CDK8-CYCC IN COMPLEX WITH 5-{5-Chloro-4-[1-(2-methoxy-ethyl)-1,8-diaza-spiro[4.5]dec-8-yl]-pyridin-3-yl}-1-methyl-1,3-dihydro-benzo[c]isothiazole 2,2-dioxide Deposited 2015-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 5Y7 5-[5-chloranyl-4-[1-(2-methoxyethyl)-1,8-diazaspiro[4.5]decan-8-yl]pyridin-3-yl]-1-methyl-3~{H}-2,1-benzothiazole 2,2-dioxide × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 2.50 Å R-free 0.268
5HBJ CDK8-CYCC IN COMPLEX WITH 8-[2-Amino-3-chloro-5-(1-methyl-1H-indazol-5-yl)-pyridin-4-yl]-2,8-diaza-spiro[4.5]decan-1-one Deposited 2015-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 5Y8 8-[2-azanyl-3-chloranyl-5-(1-methylindazol-5-yl)pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；RESERVOIR SOLUTION : pH 6.90
Resolution 3.00 Å R-free 0.288
5HNB CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone Deposited 2016-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 62M [6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone × 1 FMT FORMIC ACID × 6 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.2M lithium chloride
Resolution 2.35 Å R-free 0.252
5HVY CDK8/CYCC IN COMPLEX WITH COMPOUND 20 Deposited 2016-01-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded 66X N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea × 1 FMT FORMIC ACID × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG 3350 and 0.20 M sodium formate
Resolution 2.39 Å R-free 0.220
5I5Z CDK8-CYCC IN COMPLEX WITH 8-(1-Methyl-2,2-dioxo-2,3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-[1,6]naphthyridine-2-carboxylic acid methylamide Deposited 2016-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 68U N-methyl-8-(1-methyl-2,2-dioxo-2,3-dihydro-1H-2lambda~6~,1-benzothiazol-5-yl)-1,6-naphthyridine-2-carboxamide × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG3350, 0.2 M sodium formate, pH 6.9
Resolution 2.60 Å R-free 0.274
5ICP CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(5-methyl-imidazo[5,1-b][1,3,4]thiadiazol-2-yl)-methanone Deposited 2016-02-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 69Z [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](5-methylimidazo[5,1-b][1,3,4]thiadiazol-2-yl)methanone × 1 EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG3350, 0.2 M sodium formate, pH 6.9
Resolution 2.18 Å R-free 0.216
5IDN CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-methanone Deposited 2016-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 6A7 [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG 3350, 0.2 M sodium formate, pH 6.9
Resolution 2.26 Å R-free 0.253
5IDP CDK8-CYCC IN COMPLEX WITH (3-Amino-1H-indazol-5-yl)-[(S)-2-(4-fluoro-phenyl)-piperidin-1-yl]-methanone Deposited 2016-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded 6A6 (3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；20% PEG 3350, 0.2 M sodium formate, pH 6.9
Resolution 2.65 Å R-free 0.272
5XQX Human CDK8-CYCC in complex with compound 4: N-methyl-4-(4-pyridyl)-1H-pyrrole-2-carboxamide Deposited 2017-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–264（263 aa） Fragment：UNP residues 2-264
Not recorded GOL GLYCEROL × 2 8CC N-methyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05M MgCl, 0.1M MES pH 6.5, 10% Iso-propanol, 5% PEG4K
Resolution 2.30 Å R-free 0.222
5XS2 CDK8-CYCC IN COMPLEX WITH COMPOUND 17:3-chloro-4-(4-pyridyl)-1H-pyrrole-2-carboxamide Deposited 2017-06-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–264（263 aa） Fragment：UNP residues 2-264
Not recorded GOL GLYCEROL × 1 8D6 3-chloranyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05M MgCl, 0.1M MES pH 6.5, 10% Iso-propanol, 5% PEG4K
Resolution 2.04 Å R-free 0.225
6QTG Crystal structure of human CDK8/CYCC in complex with BI-1347 Deposited 2019-02-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded JH8 2-[4-(4-isoquinolin-4-ylphenyl)pyrazol-1-yl]-~{N},~{N}-dimethyl-ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；32-38% Morpheus Precipitant Mix 4 10 mmol/L Morpheus Buffer System 1 100 mM Morpheus Amino Acids Mix 2% DMSO
Resolution 2.70 Å R-free 0.231
6QTJ Crystal structure of human CDK8/CYCC in complex with BI 919811 Deposited 2019-02-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded JHK ~{N},~{N}-dimethyl-2-[4-[4-(2,6-naphthyridin-4-yl)phenyl]pyrazol-1-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；32-38% Morpheus Precipitant Mix 4 10 mmol/L Morpheus Buffer System 1 100 mM Morpheus Amino Acids Mix 2% DMSO
Resolution 2.48 Å R-free 0.220
6R3S CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH COMPOUND 1 Deposited 2019-03-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded JRE 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.19 Å R-free 0.227
6T41 CDK8/Cyclin C in complex with N-(4-chlorobenzyl)isoquinolin-4-amine Deposited 2019-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded MFE ~{N}-[(4-chlorophenyl)methyl]quinazolin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20%(w/v) PEG-3350 and 0.2 M sodium formate
Resolution 2.45 Å R-free 0.256
6TPA CDK8/CyclinC in complex with drug ETP-50775 Deposited 2019-12-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded NZ8 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-(5-oxidanylidene-6-pyridin-4-yl-pyrido[2,3-b][1,5]benzoxazepin-9-yl)urea × 1 FMT FORMIC ACID × 12 NZ5 (2~{R})-butane-1,2-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 3350, 200mM NaFormate, 3% Butanediol
Resolution 2.80 Å R-free 0.264
6Y0A CRYSTAL STRUCTURE OF CDK8-CycC IN COMPLEX WITH BI00690300 Deposited 2020-02-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–280（280 aa）
Not recorded JRE 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；20% (wt/vol) polyethylene glycol 3350 0.2 M sodium formate
Resolution 2.19 Å R-free 0.227
8TQ2 Structure of the kinase lobe of human CDK8 kinase module Deposited 2023-08-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–283（283 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TQC Structure of the human CDK8 kinase module Deposited 2023-08-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–283（283 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TQW Structure of human transcriptional Mediator complex Deposited 2023-08-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain b 1–283（283 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
9H8C Human CDK8/Cyclin-C complex with inhibitor 2-9 Deposited 2024-10-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 A1IS8 4-[(3~{S})-3-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]piperidin-1-yl]carbonyl-1~{H}-pyrrole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES pH6.5, HEPES pH6.8, Sodium Formate
Resolution 2.57 Å R-free 0.262
9H8S Human CDK8/Cyclin-C complex with inhibitor 3-7 Deposited 2024-10-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–283（283 aa）
Not recorded CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1 A1ITF 4-[(3~{S},5~{R})-3-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]-5-methoxy-piperidin-1-yl]carbonyl-1~{H}-pyrrole-2-carbonitrile × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES pH6.5, HEPES pH6.8, Sodium Formate
Resolution 2.16 Å R-free 0.248

35 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCNC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–287； UniProt 1–283

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4f6u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4f6u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4f6u
Deposition date deposition_date2012-05-15
Structure title titleCrystal structure of human CDK8/CYCC in complex with compound 5 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea)
Keywords keywordsprotein kinase complex, Proteros, TRANSFERASE-TRANSCRIPTION-INHIBITOR complex; TRANSFERASE/TRANSCRIPTION/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.97 Å
Radius of gyration Rg (electron density) rg_electron28.26 Å
Forward intensity I(0) i0153828000.00
Molecular weight molecular_weight67006.0 kDa
Excluded volume excluded_volume65519 ų
Envelope volume envelope_volume112730 ų
Hydration-shell volume shell_volume33179 ų
Envelope diameter envelope_diameter93.7 Å
Shell Rg shell_rg35.71 Å
Envelope Rg envelope_rg28.33 Å
Shape Rg shape_rg28.24 Å
Total Rg total_rg28.84 Å
Total atoms total_atoms5078
Residues n_residues600
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.0 Å
Rg (real space) rg_real28.95 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real1.5380e+08
I(0) uncertainty (real space) i0_real_error2.2640e+06
Rg (reciprocal space) rg_reciprocal28.96 Å
I(0) (reciprocal space) i0_reciprocal153800000.0000
Solution quality estimate total_estimate0.9030
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.7 Å
Skewness Skewness skewness0.271
Kurtosis Kurtosis kurtosis-0.598
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha34310000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.861
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4f6uA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4f6uA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4f6uB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4f6uB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
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8. Citations (1)

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9. Files and Curves (10)