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Structure paper

TitleDesign principles for cyclin K molecular glue degraders.
Journal, issue, pagesNat. Chem. Biol., Vol. 20, Page 93-102, Year 2024
Publish dateNov 30, 2022 (structure data deposition date)
AuthorsKozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. ...Kozicka, Z. / Suchyta, D.J. / Focht, V. / Kempf, G. / Petzold, G. / Jentzsch, M. / Zou, C. / Di Genua, C. / Donovan, K.A. / Coomar, S. / Cigler, M. / Mayor-Ruiz, C. / Schmid-Burgk, J.L. / Haussinger, D. / Winter, G.E. / Fischer, E.S. / Slabicki, M. / Gillingham, D. / Ebert, B.L. / Thoma, N.H.
External linksNat. Chem. Biol. / PubMed:37679459
MethodsX-ray diffraction
Resolution2.98 - 3.85 Å
Structure data

PDB-8bu1:
Structure of DDB1 bound to DS17-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 2.98 Å

PDB-8bu2:
Structure of DDB1 bound to DS18-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.13 Å

PDB-8bu3:
Structure of DDB1 bound to DS19-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.42 Å

PDB-8bu4:
Structure of DDB1 bound to DS22-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.09 Å

PDB-8bu5:
Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.134 Å

PDB-8bu6:
Structure of DDB1 bound to DS55-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.45 Å

PDB-8bu7:
Structure of DDB1 bound to 21195-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.245 Å

PDB-8bu9:
Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.51 Å

PDB-8bua:
Structure of DDB1 bound to 919278-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.193 Å

PDB-8bub:
Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.42 Å

PDB-8buc:
Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.85 Å

PDB-8bud:
Structure of DDB1 bound to Z7-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-8bue:
Structure of DDB1 bound to Z11-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.25 Å

PDB-8buf:
Structure of DDB1 bound to Z12-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-8bug:
Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.53 Å

PDB-8buh:
Structure of DDB1 bound to WX3-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.79 Å

PDB-8bui:
Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.5 Å

PDB-8buj:
Structure of DDB1 bound to DS06-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.62 Å

PDB-8buk:
Structure of DDB1 bound to DS08-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.41 Å

PDB-8bul:
Structure of DDB1 bound to DS11-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

PDB-8bum:
Structure of DDB1 bound to DS15-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.36 Å

PDB-8bun:
Structure of DDB1 bound to DS16-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.08 Å

PDB-8buo:
Structure of DDB1 bound to DS24-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.58 Å

PDB-8bup:
Structure of DDB1 bound to DS30-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.41 Å

PDB-8buq:
Structure of DDB1 bound to DS43-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-8bur:
Structure of DDB1 bound to DS50-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.64 Å

PDB-8bus:
Structure of DDB1 bound to DS59-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.26 Å

PDB-8but:
Structure of DDB1 bound to DS61-engaged CDK12-cyclin K
Method: X-RAY DIFFRACTION / Resolution: 3.25 Å

Chemicals

ChemComp-GOL:
GLYCEROL

ChemComp-RQL:
(2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol

ChemComp-SO4:
SULFATE ION

ChemComp-RVQ:
~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-RSI:
2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine

ChemComp-RMF:
~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine

ChemComp-CIT:
CITRIC ACID

ChemComp-RQE:
~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine

ChemComp-RS5:
1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one

ChemComp-RRC:
R-ROSCOVITINE / inhibitor*YM

ChemComp-RVH:
(2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide

ChemComp-RNU:
~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide

ChemComp-RKO:
2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide

ChemComp-RP9:
~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide

ChemComp-RVU:
~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide

ChemComp-RW6:
2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one

ChemComp-RPW:
2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide

ChemComp-RR9:
6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one

ChemComp-RV6:
(2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol

ChemComp-RUW:
(2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RWE:
(2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RSU:
(2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-T6X:
(2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RNF:
(2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RLC:
(2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RWN:
(2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RQ9:
(2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

ChemComp-RQU:
~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide

ChemComp-RMX:
1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide

ChemComp-RQ5:
2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol

Source
  • homo sapiens (human)
KeywordsLIGASE / kinase / cyclin / ubiquitin / degrader

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