Target Binding Site Detail
| 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 | |||||
| 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: 4F9A Human CDC7 kinase in complex with DBF4 and nucleotide | ||||||
| Method | X-ray diffraction | Resolution | 2.17 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 QQRAGTPGFR380 APEVLTKCPN390 QTTAIDMWSA 400 GVIFLSLLSG410 RYPFYKASDD420 LTALAQIMTI430 RGSRETIQAA440 KTFGKSILCS 450 KEVPAQDLRK460 LCERLRGWNE537 VPDEAYDLLD547 KLLDLNPASR557 ITAEEALLHP 567 FFKDM
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ILE64
3.877
GLY65
3.947
GLU66
4.114
GLY67
3.654
PHE69
4.670
SER70
3.216
VAL72
3.533
ALA88
3.504
LYS90
2.652
GLU104
4.876
MET118
3.245
|
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| PDB ID: 4F99 Human CDC7 kinase in complex with DBF4 and nucleotide | ||||||
| Method | X-ray diffraction | Resolution | 2.33 Å | Mutation | No | [1] |
| PDB Sequence |
KKDIEKLYEA
50 VPQLSNVFKI60 EDKIGEGTFS70 SVYLATAQLQ80 VGPEEKIALK90 HLIPTSHPIR 100 IAAELQCLTV110 AGGQDNVMGV120 KYCFRKNDHV130 VIAMPYLEHE140 SFLDILNSLS 150 FQEVREYMLN160 LFKALKRIHQ170 FGIVHRDVKP180 SNFLYNRRLK190 KYALVDFGLA 200 QGTHDTKIEL210 LKFVQSEAQQ220 RAGTPGFRAP382 EVLTKCPNQT392 TAIDMWSAGV 402 IFLSLLSGRY412 PFYKASDDLT422 ALAQIMTIRG432 SRETIQAAKT442 FGKSILCSKE 452 VPAQDLRKLC462 ERLRWNEVPD540 EAYDLLDKLL550 DLNPASRITA560 EEALLHPFFK 570 DM
|
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|
|
ILE64
3.541
GLY65
3.885
GLU66
3.873
GLY67
3.580
PHE69
4.524
SER70
2.942
VAL72
3.267
ALA88
3.505
LYS90
2.603
GLU104
4.974
MET118
3.102
|
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| PDB ID: 6YA8 Cdc7-Dbf4 bound to ADP-BeF3 | ||||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [2] |
| PDB Sequence |
AGVKKDIEKL
47 YEAVPQLSNV57 FKIEDKIGEG67 TFSSVYLATA77 QLQVGPEEKI87 ALKHLIPTSH 97 PIRIAAELQC107 LTVAGGQDNV117 MGVKYCFRKN127 DHVVIAMPYL137 EHESFLDILN 147 SLSFQEVREY157 MLNLFKALKR167 IHQFGIVHRD177 VKPSNFLYNR187 RLKKYALVDF 197 GLAQGTHDTK207 IELLKFVPAS348 LTCDCYATDK358 VCSICLSRRQ368 QVAPRAGTPG 378 FRAPEVLTKC388 PNQTTAIDMW398 SAGVIFLSLL408 SGRYPFYKAS418 DDLTALAQIM 428 TIRGSRETIQ438 AAKTFGKSIL448 CSKEVPAQDL458 RKLCERLRGA468 GGWNEVPDEA 542 YDLLDKLLDL552 NPASRITAEE562 ALLHPFFKDM572
|
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| PDB ID: 6YA7 Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate | ||||||
| Method | X-ray diffraction | Resolution | 1.67 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 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 #f3c393; 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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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of human CDC7 kinase in complex with its activator DBF4. Nat Struct Mol Biol. 2012 Nov;19(11):1101-7. | ||||
| REF 2 | Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase. Structure. 2020 Aug 4;28(8):954-962.e4. | ||||
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