Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T81358 | Target Info | |||
| Target Name | CDC7-related kinase (CDC7) | ||||
| Synonyms | huCdc7; HsCdc7; Cell division cycle 7related protein kinase; Cell division cycle 7-related protein kinase; CDC7related kinase; CDC7L1 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CDC7 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Boric acid | Ligand Info | |||||
| Structure Description | Minimal construct of Cdc7-Dbf4 bound to XL413 | PDB:6YA6 | ||||
| Method | X-ray diffraction | Resolution | 1.44 Å | Mutation | No | [1] |
| PDB Sequence |
AGVKKDIEKL
47 YEAVPQLSNV57 FKIEDKIGEG67 TFSSVYLATA77 QLQVGPEEKI87 ALKHLIPTSH 97 PIRIAAELQC107 LTVAGGQDNV117 MGVKYCFRKN127 DHVVIAMPYL137 EHESFLDILN 147 SLSFQEVREY157 MLNLFKALKR167 IHQFGIVHRD177 VKPSNFLYNR187 RLKKYALVDF 197 GLAQGTHDTK207 IELLKFVQPA347 SLTCDCYATD357 KVCSICLSRR367 QQVAPRAGTP 377 GFRAPEVLTK387 CPNQTTAIDM397 WSAGVIFLSL407 LSGRYPFYKA417 SDDLTALAQI 427 MTIRGSRETI437 QAAKTFGKSI447 LCSKEVPAQD457 LRKLCERLRG467 AGAGGWNEVP 539 DEAYDLLDKL549 LDLNPASRIT559 AEEALLHPFF569 KDMS
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| Ligand Name: BMS-863233 | Ligand Info | |||||
| Structure Description | Minimal construct of Cdc7-Dbf4 bound to XL413 | PDB:6YA6 | ||||
| Method | X-ray diffraction | Resolution | 1.44 Å | Mutation | No | [1] |
| PDB Sequence |
AGVKKDIEKL
47 YEAVPQLSNV57 FKIEDKIGEG67 TFSSVYLATA77 QLQVGPEEKI87 ALKHLIPTSH 97 PIRIAAELQC107 LTVAGGQDNV117 MGVKYCFRKN127 DHVVIAMPYL137 EHESFLDILN 147 SLSFQEVREY157 MLNLFKALKR167 IHQFGIVHRD177 VKPSNFLYNR187 RLKKYALVDF 197 GLAQGTHDTK207 IELLKFVQPA347 SLTCDCYATD357 KVCSICLSRR367 QQVAPRAGTP 377 GFRAPEVLTK387 CPNQTTAIDM397 WSAGVIFLSL407 LSGRYPFYKA417 SDDLTALAQI 427 MTIRGSRETI437 QAAKTFGKSI447 LCSKEVPAQD457 LRKLCERLRG467 AGAGGWNEVP 539 DEAYDLLDKL549 LDLNPASRIT559 AEEALLHPFF569 KDMS
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ILE64
4.004
GLY65
3.841
GLU66
3.781
GLY67
3.716
SER70
3.268
VAL72
3.661
ALA88
3.294
LYS90
2.769
GLU104
4.369
MET118
3.781
MET134
3.241
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: PHA-767491 | Ligand Info | |||||
| Structure Description | Human CDC7 kinase in complex with DBF4 and PHA767491 | PDB:4F9B | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [2] |
| PDB Sequence |
GVKKDIEKLY
48 EAVPQLSNVF58 KIEDKIGEGT68 FSSVYLATAQ78 LQVGPEEKIA88 LKHLIPTSHP 98 IRIAAELQCL108 TVAGGQDNVM118 GVKYCFRKND128 HVVIAMPYLE138 HESFLDILNS 148 LSFQEVREYM158 LNLFKALKRI168 HQFGIVHRDV178 KPSNFLYNRR188 LKKYALVDFG 198 LAQGTHDTKI208 ELLKFVQSEA218 QQVAPRAGTP377 GFRAPEVLTK387 CPNQTTAIDM 397 WSAGVIFLSL407 LSGRYPFYKA417 SDDLTALAQI427 MTIRGSRETI437 QAAKTFGKSI 447 LCSKEVPAQD457 LRKLCERLRG534 WNEVPDEAYD544 LLDKLLDLNP554 ASRITAEEAL 564 LHPFFKDM
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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 .0SY or .0SY2 or .0SY3 or :30SY;style chemicals stick;color identity;select .A:64 or .A:70 or .A:72 or .A:88 or .A:90 or .A:104 or .A:118 or .A:134 or .A:135 or .A:136 or .A:137 or .A:139 or .A:181 or .A:182 or .A:184 or .A:195 or .A:196; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: L-serine-O-phosphate | Ligand Info | |||||
| Structure Description | Minimal construct of Cdc7-Dbf4 bound to XL413 | PDB:6YA6 | ||||
| Method | X-ray diffraction | Resolution | 1.44 Å | Mutation | No | [1] |
| PDB Sequence |
AGVKKDIEKL
47 YEAVPQLSNV57 FKIEDKIGEG67 TFSSVYLATA77 QLQVGPEEKI87 ALKHLIPTSH 97 PIRIAAELQC107 LTVAGGQDNV117 MGVKYCFRKN127 DHVVIAMPYL137 EHESFLDILN 147 SLSFQEVREY157 MLNLFKALKR167 IHQFGIVHRD177 VKPSNFLYNR187 RLKKYALVDF 197 GLAQGTHDTK207 IELLKFVQPA347 SLTCDCYATD357 KVCSICLSRR367 QQVAPRAGTP 377 GFRAPEVLTK387 CPNQTTAIDM397 WSAGVIFLSL407 LSGRYPFYKA417 SDDLTALAQI 427 MTIRGSRETI437 QAAKTFGKSI447 LCSKEVPAQD457 LRKLCERLRG467 AGAGGWNEVP 539 DEAYDLLDKL549 LDLNPASRIT559 AEEALLHPFF569 KDMS
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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 .SEP or .SEP2 or .SEP3 or :3SEP;style chemicals stick;color identity;select .A:350 or .A:369 or .A:444; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate | PDB:6YA7 | ||||
| Method | X-ray diffraction | Resolution | 1.67 Å | Mutation | No | [1] |
| PDB Sequence |
GVKKDIEKLY
48 EAVPQLSNVF58 KIEDKIGEGT68 FSSVYLATAQ78 LQVGPEEKIA88 LKHLIPTSHP 98 IRIAAELQCL108 TVAGGQDNVM118 GVKYCFRKND128 HVVIAMPYLE138 HESFLDILNS 148 LSFQEVREYM158 LNLFKALKRI168 HQFGIVHRDV178 KPSNFLYNRR188 LKKYALVDFG 198 LAQGTHDTKI208 ELLKFVQSEA218 QQERPASLTC351 DCYATDKVCS361 ICLSRRQQVA 371 PRAGTPGFRA381 PEVLTKCPNQ391 TTAIDMWSAG401 VIFLSLLSGR411 YPFYKASDDL 421 TALAQIMTIR431 GSRETIQAAK441 TFGKSILCSK451 EVPAQDLRKL461 CERLRGAGAG 471 GWNEVPDEAY543 DLLDKLLDLN553 PASRITAEEA563 LLHPFFKDMS573 |
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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:64 or .A:65 or .A:66 or .A:67 or .A:68 or .A:69 or .A:70 or .A:71 or .A:72 or .A:88 or .A:90 or .A:118 or .A:134 or .A:135 or .A:136 or .A:137 or .A:139 or .A:181 or .A:182 or .A:184 or .A:195 or .A:196; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE64
3.820
GLY65
3.986
GLU66
3.983
GLY67
3.061
THR68
4.485
PHE69
4.679
SER70
2.629
SER71
4.458
VAL72
3.552
ALA88
3.477
LYS90
3.185
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3-((2-Mercaptoacetyl)amino)-L-alanine | Ligand Info | |||||
| Structure Description | Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate | PDB:6YA7 | ||||
| Method | X-ray diffraction | Resolution | 1.67 Å | Mutation | No | [1] |
| PDB Sequence |
GVKKDIEKLY
48 EAVPQLSNVF58 KIEDKIGEGT68 FSSVYLATAQ78 LQVGPEEKIA88 LKHLIPTSHP 98 IRIAAELQCL108 TVAGGQDNVM118 GVKYCFRKND128 HVVIAMPYLE138 HESFLDILNS 148 LSFQEVREYM158 LNLFKALKRI168 HQFGIVHRDV178 KPSNFLYNRR188 LKKYALVDFG 198 LAQGTHDTKI208 ELLKFVQSEA218 QQERPASLTC351 DCYATDKVCS361 ICLSRRQQVA 371 PRAGTPGFRA381 PEVLTKCPNQ391 TTAIDMWSAG401 VIFLSLLSGR411 YPFYKASDDL 421 TALAQIMTIR431 GSRETIQAAK441 TFGKSILCSK451 EVPAQDLRKL461 CERLRGAGAG 471 GWNEVPDEAY543 DLLDKLLDLN553 PASRITAEEA563 LLHPFFKDMS573 |
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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 .7O5 or .7O52 or .7O53 or :37O5;style chemicals stick;color identity;select .A:67 or .A:68 or .A:69 or .A:177 or .A:179 or .A:181 or .A:182 or .A:196 or .A:199 or .A:375 or .A:376; 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 | Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase. Structure. 2020 Aug 4;28(8):954-962.e4. | ||||
| REF 2 | Crystal structure of human CDC7 kinase in complex with its activator DBF4. Nat Struct Mol Biol. 2012 Nov;19(11):1101-7. | ||||
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