Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T51565 | Target Info | |||
| Target Name | Casein kinase II alpha (CSNK2A1) | ||||
| Synonyms | Protein kinase CK2; Casein kinase II subunit alpha; CK2A1; CK II alpha; CK II | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CSNK2A1 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | adenosine diphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N | ||||
| InChI | 1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 | ||||
| InChIKey | XTWYTFMLZFPYCI-KQYNXXCUSA-N | ||||
| PubChem Compound ID | 6022 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6YZH Crystal structure of P8C9 bound to CK2alpha | ||||||
| Method | X-ray diffraction | Resolution | 1.19 Å | Mutation | No | [1] |
| PDB Sequence |
GGRLVPRFGE
-3 GEGSEGPVPS7 RARVYTDVNT17 HRPSEYWDYE27 SHVVEWGNQD37 DYQLVRKLGR 47 GKYSEVFEAI57 NITNNEKVVV67 KILKPVKKKK77 IKREIKILEN87 LRGGPNIITL 97 ADIVKDPVSR107 TPALVFEHVN117 NTDFKQLYQT127 LTDYDIRFYM137 YEILKALDYC 147 HSMGIMHRDV157 KPHNVMIDHE167 HRKLRLIDWG177 LAEFYHPGQE187 YNVRVASRYF 197 KGPELLVDYQ207 MYDYSLDMWS217 LGCMLASMIF227 RKEPFFHGHD237 NYDQLVRIAK 247 VLGTEDLYDY257 IDKYNIELDP267 RFNDILGRHS277 RKRWERFVHS287 ENQHLVSPEA 297 LDFLDKLLRY307 DHQSRLTARE317 AMEHPYFYTV327 VKEN
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| PDB ID: 5CVH Crystal Structure of CK2alpha | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | Yes | [2] |
| PDB Sequence |
SGPVPSRARV
11 YTDVNTHRPS21 EYWDYESHVV31 EWGNQDDYQL41 VRKLGRGKYS51 EVFEAINITN 61 NEKVVVKILK71 PVKKKKIKRE81 IKILENLRGG91 PNIITLADIV101 KDPVSRTPAL 111 VFEHVNNTDF121 KQLYQTLTDY131 DIRFYMYEIL141 KALDYCHSMG151 IMHRDVKPHN 161 VMIDHEHRKL171 RLIDWGLAEF181 YHPGQEYNVR191 VASRYFKGPE201 LLVDYQMYDY 211 SLDMWSLGCM221 LASMIFRKEP231 FFHGHDNYDQ241 LVRIAKVLGT251 EDLYDYIDKY 261 NIELDPRFND271 ILGRHSRKRW281 ERFVHSENQH291 LVSPEALDFL301 DKLLRYDHQS 311 RLTAREAMEH321 PYFYTVV
|
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|
LEU45
3.712
GLY46
4.143
ARG47
3.672
GLY48
3.571
LYS49
4.088
TYR50
3.317
SER51
2.423
VAL53
3.471
VAL66
3.622
LYS68
2.952
ILE95
3.379
|
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| PDB ID: 5MOE Crystal Structure of CK2alpha with N-(3-(((2-chloro-[1,1'-biphenyl]-4-yl)methyl)amino)propyl)methanesulfonamide bound | ||||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | Yes | [3] |
| PDB Sequence |
GPVPSRARVY
12 TDVNTHRPSE22 YWDYESHVVE32 WGNQDDYQLV42 RKLGRGKYSE52 VFEAINITNN 62 EKVVVKILKP72 VKKKKIKREI82 KILENLRGGP92 NIITLADIVK102 DPVSRTPALV 112 FEHVNNTDFK122 QLYQTLTDYD132 IRFYMYEILK142 ALDYCHSMGI152 MHRDVKPHNV 162 MIDHEHRKLR172 LIDWGLAEFY182 HPGQEYNVRV192 ASRYFKGPEL202 LVDYQMYDYS 212 LDMWSLGCML222 ASMIFRKEPF232 FHGHDNYDQL242 VRIAKVLGTE252 DLYDYIDKYN 262 IELDPRFNDI272 LGRHSRKRWE282 RFVHSENQHL292 VSPEALDFLD302 KLLRYDHQSR 312 LTAREAMEHP322 YFYTV
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| PDB ID: 5MP8 Crystal Structure of CK2alpha with ZT0432 bound | ||||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | Yes | [3] |
| PDB Sequence |
GPVPSRARVY
12 TDVNTHRPSE22 YWDYESHVVE32 WGNQDDYQLV42 RKLGRGKYSE52 VFEAINITNN 62 EKVVVKILKP72 VKKKKIKREI82 KILENLRGGP92 NIITLADIVK102 DPVSRTPALV 112 FEHVNNTDFK122 QLYQTLTDYD132 IRFYMYEILK142 ALDYCHSMGI152 MHRDVKPHNV 162 MIDHEHRKLR172 LIDWGLAEFY182 HPGQEYNVRV192 ASRYFKGPEL202 LVDYQMYDYS 212 LDMWSLGCML222 ASMIFRKEPF232 FHGHDNYDQL242 VRIAKVLGTE252 DLYDYIDKYN 262 IELDPRFNDI272 LGRHSRKRWE282 RFVHSENQHL292 VSPEALDFLD302 KLLRYDHQSR 312 LTAREAMEHP322 YFYTV
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:53 or .A:66 or .A:68 or .A:95 or .A:113 or .A:114 or .A:115 or .A:116 or .A:118 or .A:160 or .A:161 or .A:163 or .A:174 or .A:175; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU45
4.012
GLY46
4.106
ARG47
4.752
GLY48
3.130
LYS49
3.260
TYR50
3.768
SER51
2.595
VAL53
3.241
VAL66
3.456
LYS68
3.365
ILE95
3.366
|
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| PDB ID: 5ORJ The crystal structure of CK2alpha in complex with compound 3 | ||||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | Yes | [4] |
| PDB Sequence |
PVPSRARVYT
13 DVNTHRPSEY23 WDYESHVVEW33 GNQDDYQLVR43 KLGRGKYSEV53 FEAINITNNE 63 KVVVKILKPV73 KKKKIKREIK83 ILENLRGGPN93 IITLADIVKD103 PVSRTPALVF 113 EHVNNTDFKQ123 LYQTLTDYDI133 RFYMYEILKA143 LDYCHSMGIM153 HRDVKPHNVM 163 IDHEHRKLRL173 IDWGLAEFYH183 PGQEYNVRVA193 SRYFKGPELL203 VDYQMYDYSL 213 DMWSLGCMLA223 SMIFRKEPFF233 HGHDNYDQLV243 RIAKVLGTED253 LYDYIDKYNI 263 ELDPRFNDIL273 GRHSRKRWER283 FVHSENQHLV293 SPEALDFLDK303 LLRYDHQSRL 313 TAREAMEHPY323 FYTV
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .B:45 or .B:46 or .B:47 or .B:48 or .B:49 or .B:50 or .B:51 or .B:53 or .B:66 or .B:68 or .B:95 or .B:113 or .B:114 or .B:115 or .B:116 or .B:118 or .B:160 or .B:161 or .B:163 or .B:174 or .B:175; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU45
4.123
GLY46
4.183
ARG47
4.842
GLY48
3.247
LYS49
3.371
TYR50
3.475
SER51
2.699
VAL53
3.447
VAL66
3.597
LYS68
3.118
ILE95
3.304
|
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| PDB ID: 5MPJ 1-(2-chloro-[1,1'-biphenyl]-4-yl)-N-methylethanamine | ||||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | Yes | [3] |
| PDB Sequence |
GPVPSRARVY
12 TDVNTHRPSE22 YWDYESHVVE32 WGNQDDYQLV42 RKLGRGKYSE52 VFEAINITNN 62 EKVVVKILKP72 VKKKKIKREI82 KILENLRGGP92 NIITLADIVK102 DPVSRTPALV 112 FEHVNNTDFK122 QLYQTLTDYD132 IRFYMYEILK142 ALDYCHSMGI152 MHRDVKPHNV 162 MIDHEHRKLR172 LIDWGLAEFY182 HPGQEYNVRV192 ASRYFKGPEL202 LVDYQMYDYS 212 LDMWSLGCML222 ASMIFRKEPF232 FHGHDNYDQL242 VRIAKVLGTE252 DLYDYIDKYN 262 IELDPRFNDI272 LGRHSRKRWE282 RFVHSENQHL292 VSPEALDFLD302 KLLRYDHQSR 312 LTAREAMEHP322 YFYTVV
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:45 or .A:46 or .A:48 or .A:49 or .A:50 or .A:51 or .A:53 or .A:66 or .A:68 or .A:95 or .A:113 or .A:114 or .A:115 or .A:116 or .A:118 or .A:160 or .A:161 or .A:163 or .A:174 or .A:175; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 5ORK The crystal structure of CK2alpha in complex with compound 6 | ||||||
| Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | Yes | [4] |
| PDB Sequence |
PVPSRARVYT
13 DVNTHRPSEY23 WDYESHVVEW33 GNQDDYQLVR43 KLGRGKYSEV53 FEAINITNNE 63 KVVVKILKPV73 KKKKIKREIK83 ILENLRGGPN93 IITLADIVKD103 PVSRTPALVF 113 EHVNNTDFKQ123 LYQTLTDYDI133 RFYMYEILKA143 LDYCHSMGIM153 HRDVKPHNVM 163 IDHEHRKLRL173 IDWGLAEFYH183 PGQEYNVRVA193 SRYFKGPELL203 VDYQMYDYSL 213 DMWSLGCMLA223 SMIFRKEPFF233 HGHDNYDQLV243 RIAKVLGTED253 LYDYIDKYNI 263 ELDPRFNDIL273 GRHSRKRWER283 FVHSENQHLV293 SPEALDFLDK303 LLRYDHQSRL 313 TAREAMEHPY323 FYT
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .B:45 or .B:46 or .B:48 or .B:49 or .B:50 or .B:51 or .B:53 or .B:66 or .B:68 or .B:95 or .B:113 or .B:114 or .B:115 or .B:116 or .B:118 or .B:160 or .B:161 or .B:163 or .B:174 or .B:175; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 5OQU The crystal structure of CK2alpha in complex with compound 5 | ||||||
| Method | X-ray diffraction | Resolution | 2.32 Å | Mutation | Yes | [4] |
| PDB Sequence |
PVPSRARVYT
13 DVNTHRPSEY23 WDYESHVVEW33 GNQDDYQLVR43 KLGRGKYSEV53 FEAINITNNE 63 KVVVKILKPV73 KKKKIKREIK83 ILENLRGGPN93 IITLADIVKD103 PVSRTPALVF 113 EHVNNTDFKQ123 LYQTLTDYDI133 RFYMYEILKA143 LDYCHSMGIM153 HRDVKPHNVM 163 IDHEHRKLRL173 IDWGLAEFYH183 PGQEYNVRVA193 SRYFKGPELL203 VDYQMYDYSL 213 DMWSLGCMLA223 SMIFRKEPFF233 HGHDNYDQLV243 RIAKVLGTED253 LYDYIDKYNI 263 ELDPRFNDIL273 GRHSRKRWER283 FVHSENQHLV293 SPEALDFLDK303 LLRYDHQSRL 313 TAREAMEHPY323 FYTV
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .B:45 or .B:46 or .B:47 or .B:48 or .B:49 or .B:51 or .B:53 or .B:66 or .B:68 or .B:95 or .B:113 or .B:114 or .B:115 or .B:116 or .B:118 or .B:160 or .B:161 or .B:163 or .B:174 or .B:175; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 5OSL The crystal structure of CK2alpha in complex with compound 7 | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | Yes | [4] |
| PDB Sequence |
SGPVPSRARV
11 YTDVNTHRPS21 EYWDYESHVV31 EWGNQDDYQL41 VRKLGRGKYS51 EVFEAINITN 61 NEKVVVKILK71 PVAAAKIKRE81 IKILENLRGG91 PNIITLADIV101 KDPVSRTPAL 111 VFEHVNNTDF121 KQLYQTLTDY131 DIRFYMYEIL141 KALDYCHSMG151 IMHRDVKPHN 161 VMIDHEHRKL171 RLIDWGLAEF181 YHPGQEYNVR191 VASRYFKGPE201 LLVDYQMYDY 211 SLDMWSLGCM221 LASMIFRKEP231 FFHGHDNYDQ241 LVRIAKVLGT251 EDLYDYIDKY 261 NIELDPRFND271 ILGRHSRKRW281 ERFVHSENQH291 LVSPEALDFL301 DKLLRYDHQS 311 RLTAREAMEH321 PYFYTVVK
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:45 or .A:50 or .A:51 or .A:53 or .A:66 or .A:68 or .A:95 or .A:113 or .A:114 or .A:115 or .A:116 or .A:118 or .A:160 or .A:161 or .A:163 or .A:174 or .A:175; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6YPN Crystal Structure of CK2alpha with 2 molecules of ADP bound | ||||||
| Method | X-ray diffraction | Resolution | 1.58 Å | Mutation | No | [5] |
| PDB Sequence |
SGPVPSRARV
11 YTDVNTHRPR21 EYWDYESHVV31 EWGNQDDYQL41 VRKLGRGKYS51 EVFEAINITN 61 NEKVVVKILK71 PVKKKKIKRE81 IKILENLRGG91 PNIITLADIV101 KDPVSRTPAL 111 VFEHVNNTDF121 KQLYQTLTDY131 DIRFYMYEIL141 KALDYCHSMG151 IMHRDVKPHN 161 VMIDHEHRKL171 RLIDWGLAEF181 YHPGQEYNVR191 VASRYFKGPE201 LLVDYQMYDY 211 SLDMWSLGCM221 LASMIFRKEP231 FFHGHDNYDQ241 LVRIAKVLGT251 EDLYDYIDKY 261 NIELDPRFND271 ILGRHSRKRW281 ERFVHSENQH291 LVSPEALDFL301 DKLLRYDHQS 311 RLTAREAMEH321 PYFYTV
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .B:45 or .B:48 or .B:50 or .B:51 or .B:53 or .B:66 or .B:68 or .B:74 or .B:77 or .B:80 or .B:95 or .B:113 or .B:114 or .B:115 or .B:116 or .B:118 or .B:155 or .B:156 or .B:160 or .B:161 or .B:163 or .B:174 or .B:175 or .B:177 or .B:178 or .B:180 or .B:189 or .B:191 or .B:192 or .B:193; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU45
4.110
GLY48
4.844
TYR50
3.215
SER51
2.578
VAL53
3.411
VAL66
3.693
LYS68
2.735
LYS74
4.359
LYS77
2.594
ARG80
2.668
ILE95
3.591
PHE113
4.086
GLU114
2.871
HIS115
4.007
VAL116
3.129
|
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| PDB ID: 7ZY0 Crystal structure of compound 7 bound to CK2alpha | ||||||
| Method | X-ray diffraction | Resolution | 1.44 Å | Mutation | Yes | [6] |
| PDB Sequence |
GPVPSRARVY
12 TDVNTHRPSE22 YWDYESHVVE32 WGNQDDYQLV42 RKLGRGKYSE52 VFEAINITNN 62 EKVVVKILKP72 VAAAKIKREI82 KILENLRGGP92 NIITLADIVK102 DPVSRTPALV 112 FEHVNNTDFK122 QLYQTLTDYD132 IRFYMYEILK142 ALDYCHSMGI152 MHRDVKPHNV 162 MIDHEHRKLR172 LIDWGLAEFY182 HPGQEYNVRV192 ASRYFKGPEL202 LVDYQMYDYS 212 LDMWSLGCML222 ASMIFRKEPF232 FHGHDNYDQL242 VRIAKVLGTE252 DLYDYIDKYN 262 IELDPRFNDI272 LGRHSRKRWE282 RFVHSENQHL292 VSPEALDFLD302 KLLRYDHQSR 312 LTAREAMEHP322 YFYTVVK
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:51 or .A:53 or .A:66 or .A:68 or .A:95 or .A:113 or .A:114 or .A:115 or .A:116 or .A:118 or .A:163 or .A:174 or .A:175; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6Z19 Crystal structure of P8C9 bound to CK2alpha | ||||||
| Method | X-ray diffraction | Resolution | 1.47 Å | Mutation | No | [1] |
| PDB Sequence |
SGPVPSRARV
11 YTDVNTHRPR21 EYWDYESHVV31 EWGNQDDYQL41 VRKLGRGKYS51 EVFEAINITN 61 NEKVVVKILK71 PVKKKKIKRE81 IKILENLRGG91 PNIITLADIV101 KDPVSRTPAL 111 VFEHVNNTDF121 KQLYQTLTDY131 DIRFYMYEIL141 KALDYCHSMG151 IMHRDVKPHN 161 VMIDHEHRKL171 RLIDWGLAEF181 YHPGQEYNVR191 VASRYFKGPE201 LLVDYQMYDY 211 SLDMWSLGCM221 LASMIFRKEP231 FFHGHDNYDQ241 LVRIAKVLGT251 EDLYDYIDKY 261 NIELDPRFND271 ILGRHSRKRW281 ERFVHSENQH291 LVSPEALDFL301 DKLLRYDHQS 311 RLTAREAMEH321 PYFYTVVK
|
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .B:45 or .B:46 or .B:51 or .B:53 or .B:66 or .B:68 or .B:95 or .B:113 or .B:114 or .B:115 or .B:116 or .B:118 or .B:160 or .B:161 or .B:163 or .B:174 or .B:175; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Development of small cyclic peptides targeting the CK2 alpha / beta interface. Chem Commun (Camb). 2022 Apr 12;58(30):4791-4794. | ||||
| REF 2 | Specific inhibition of CK2Alpha from an anchor outside the active site. Chem Sci. 2016 Nov 1;7(11):6839-6845. | ||||
| REF 3 | A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066. Bioorg Med Chem. 2017 Jul 1;25(13):3471-3482. | ||||
| REF 4 | Second-generation CK2Alpha inhibitors targeting the AlphaD pocket. Chem Sci. 2018 Feb 20;9(11):3041-3049. | ||||
| REF 5 | Proposed Allosteric Inhibitors Bind to the ATP Site of CK2Alpha. J Med Chem. 2020 Nov 12;63(21):12786-12798. | ||||
| REF 6 | A fragment-based approach leading to the discovery of inhibitors of CK2Alpha with a novel mechanism of action. RSC Med Chem. 2022 Sep 16;13(11):1420-1426. | ||||
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