2025-05-03_00000145|ligand|9JK1

Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118; X-ray diffraction 2.72Å
Protein #1 340 residues (93% resolved)

GATESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPY(TPO)NKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQRQ

GATESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQRQ
Protein #2 269 residues (88% resolved)

GAMKENKENSSPSVTSANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH

GAMKENKENSSPSVTSANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH
Non polymer #3 A1EB3

InChI=1S/C36H46N8O2/c1-4-35(45)41-32-22-31(15-16-33(32)43-20-18-29(19-21-43)42(2)3)44(36(46)39-24-26-8-6-5-7-9-26)30-13-11-28(12-14-30)40-34-17-10-27(23-37)25-38-34/h5-10,15-17,22,25,28-30H,4,11-14,18-21,24H2,1-3H3,(H,38,40)(H,39,46)(H,41,45)/t28-,30-

CCC(=O)Nc1cc(ccc1N2CCC(CC2)N(C)C)N(C3CCC(CC3)Nc4ccc(cn4)C#N)C(=O)NCc5ccccc5
Non polymer #4 EDO

InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2

C(CO)O
Non polymer #5 MG

InChI=1S/Mg/q+2

[Mg+2]
Non polymer #6 PEG

InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2

C(COCCO)O
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Reference