Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T74839 | Target Info | |||
| Target Name | Cyclin-dependent kinase 13 (CDK13) | ||||
| Synonyms | CDC2-related protein kinase 5; Cell division cycle 2-like protein kinase 5; Cell division protein kinase 13; hCDK13; Cholinesterase-related cell division controller | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | CDK13 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride | PDB:5EFQ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
IDWGKRCVDK
704 FDIIGIIGEG714 TYGQVYKARD724 KDTGEMVALK734 KVRLDNEKEG744 FPITAIREIK 754 ILRQLTHQSI764 INMKEIVTDK774 EGAFYLVFEY793 MDHDLMGLLE803 SGLVHFNENH 813 IKSFMRQLME823 GLDYCHKKNF833 LHRDIKCSNI843 LLNNRGQIKL853 ADFGLARLYS 863 SEESRPYNKV874 ITLWYRPPEL884 LLGEERYTPA894 IDVWSCGCIL904 GELFTKKPIF 914 QANQELAQLE924 LISRICGSPC934 PAVWPDVIKL944 PYFNTMKPKK954 QYRRKLREEF 964 VFIPAAALDL974 FDYMLALDPS984 KRCTAEQALQ994 CEFLRDVEPS1004 KMPPPDLPLW 1014 QDCHELWSKK1024 R
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ILE711
3.680
GLY712
3.991
GLU713
3.779
GLY714
3.133
THR715
3.086
VAL719
3.789
ALA732
3.412
LYS734
3.165
GLU752
4.902
ILE765
4.021
PHE791
3.654
|
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| Ligand Name: Phosphonothreonine | Ligand Info | |||||
| Structure Description | Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride | PDB:5EFQ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
IDWGKRCVDK
704 FDIIGIIGEG714 TYGQVYKARD724 KDTGEMVALK734 KVRLDNEKEG744 FPITAIREIK 754 ILRQLTHQSI764 INMKEIVTDK774 EGAFYLVFEY793 MDHDLMGLLE803 SGLVHFNENH 813 IKSFMRQLME823 GLDYCHKKNF833 LHRDIKCSNI843 LLNNRGQIKL853 ADFGLARLYS 863 SEESRPYNKV874 ITLWYRPPEL884 LLGEERYTPA894 IDVWSCGCIL904 GELFTKKPIF 914 QANQELAQLE924 LISRICGSPC934 PAVWPDVIKL944 PYFNTMKPKK954 QYRRKLREEF 964 VFIPAAALDL974 FDYMLALDPS984 KRCTAEQALQ994 CEFLRDVEPS1004 KMPPPDLPLW 1014 QDCHELWSKK1024 R
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Aluminum fluoride | Ligand Info | |||||
| Structure Description | Crystal structure of human Cdk13/Cyclin K in complex with ADP-aluminum fluoride | PDB:5EFQ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
IDWGKRCVDK
704 FDIIGIIGEG714 TYGQVYKARD724 KDTGEMVALK734 KVRLDNEKEG744 FPITAIREIK 754 ILRQLTHQSI764 INMKEIVTDK774 EGAFYLVFEY793 MDHDLMGLLE803 SGLVHFNENH 813 IKSFMRQLME823 GLDYCHKKNF833 LHRDIKCSNI843 LLNNRGQIKL853 ADFGLARLYS 863 SEESRPYNKV874 ITLWYRPPEL884 LLGEERYTPA894 IDVWSCGCIL904 GELFTKKPIF 914 QANQELAQLE924 LISRICGSPC934 PAVWPDVIKL944 PYFNTMKPKK954 QYRRKLREEF 964 VFIPAAALDL974 FDYMLALDPS984 KRCTAEQALQ994 CEFLRDVEPS1004 KMPPPDLPLW 1014 QDCHELWSKK1024 R
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AF3 or .AF32 or .AF33 or :3AF3;style chemicals stick;color identity;select .A:715 or .A:837 or .A:839 or .A:841 or .A:842 or .A:855 or .A:858; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[4-[(3r)-3-[[5-Chloranyl-4-(1h-Indol-3-Yl)pyrimidin-2-Yl]amino]piperidin-1-Yl]carbonylphenyl]-4-(Dimethylamino)butanamide | Ligand Info | |||||
| Structure Description | Crystal structure of human Cdk13/Cyclin K in complex with the inhibitor THZ531 | PDB:7NXJ | ||||
| Method | X-ray diffraction | Resolution | 2.36 Å | Mutation | No | [2] |
| PDB Sequence |
IDWGKRCVDK
704 FDIIGIIGEG714 TYGQVYKARD724 KDTGEMVALK734 KVRLDNEKEG744 FPITAIREIK 754 ILRQLTHQSI764 INMKEIVTDK774 EDKKDKGAFY788 LVFEYMDHDL798 MGLLESGLVH 808 FNENHIKSFM818 RQLMEGLDYC828 HKKNFLHRDI838 KCSNILLNNR848 GQIKLADFGL 858 ARLYSSEESR868 PYNKVITLWY879 RPPELLLGEE889 RYTPAIDVWS899 CGCILGELFT 909 KKPIFQANQE919 LAQLELISRI929 CGSPCPAVWP939 DVIKLPYFNT949 MKPKKQYRRK 959 LREEFVFIPA969 AALDLFDYML979 ALDPSKRCTA989 EQALQCEFLR999 DVEPSKMPPP 1009 DLPLWQDCHE1019 LWSK
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5I1 or .5I12 or .5I13 or :35I1;style chemicals stick;color identity;select .A:711 or .A:712 or .A:713 or .A:714 or .A:719 or .A:732 or .A:734 or .A:765 or .A:791 or .A:792 or .A:793 or .A:794 or .A:795 or .A:796 or .A:797 or .A:799 or .A:803 or .A:844 or .A:854 or .A:855 or .A:1015 or .A:1016 or .A:1017 or .A:1019; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE711
3.523
GLY712
4.297
GLU713
3.949
GLY714
4.745
VAL719
4.088
ALA732
3.812
LYS734
4.042
ILE765
3.608
PHE791
3.739
GLU792
3.443
TYR793
3.641
MET794
2.717
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural and Functional Analysis of the Cdk13/Cyclin K Complex. Cell Rep. 2016 Jan 12;14(2):320-31. | ||||
| REF 2 | Structure-activity relationship study of THZ531 derivatives enables the discovery of BSJ-01-175 as a dual CDK12/13 covalent inhibitor with efficacy in Ewing sarcoma. Eur J Med Chem. 2021 Oct 5;221:113481. | ||||
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