Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T42447 | Target Info | |||
| Target Name | Doublecortin-like kinase 1 (DCLK1) | ||||
| Synonyms | Serine/threonine-protein kinase DCLK1; KIAA0369; Doublecortin-like and CAM kinase-like 1; Doublecortin domain-containing protein 3A; DCDC3A; DCAMKL1 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | DCLK1 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Ruxolitinib | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1 kinase domain in complex with ruxolitinib | PDB:7F3G | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] |
| PDB Sequence |
SEEGFQIPAT
385 ITERYKVGRT395 IGDGNFAVVK405 ECVERSTARE415 YALKIIKKSK425 CRGKEHMIQN 435 EVSILRRVKH445 PNIVLLIEEM455 DVPTELYLVM465 ELVKGGDLFD475 AITSTNKYTE 485 RDASGMLYNL495 ASAIKYLHSL505 NIVHRDIKPE515 NLLVYEHQDG525 SKSLKLGDFG 535 LATIVDGPLY545 TVCGTPTYVA555 PEIIAETGYG565 LKVDIWAAGV575 ITYILLCGFP 585 PFRGSGDDQE595 VLFDQILMGQ605 VDFPSPYWDN615 VSDSAKELIT625 MMLLVDVDQR 635 FSAVQVLEHP645 WVN
|
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ILE396
3.518
GLY397
3.557
ASP398
3.728
GLY399
4.215
ALA402
3.982
VAL403
4.574
VAL404
3.527
ALA417
3.348
LYS419
3.685
VAL449
3.336
|
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| Ligand Name: NVP-TAE684 | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1-KD in complex with NVP-TAE684 | PDB:5JZN | ||||
| Method | X-ray diffraction | Resolution | 2.85 Å | Mutation | No | [2] |
| PDB Sequence |
GFQIPATITE
388 RYKVGRTIGD398 GNFAVVKECV408 ERSTAREYAL418 KIIKKSKCRG428 KEHMIQNEVS 438 ILRRVKHPNI448 VLLIEEMDVP458 TELYLVMELV468 KGGDLFDAIT478 STNKYTERDA 488 SGMLYNLASA498 IKYLHSLNIV508 HRDIKPENLL518 VYEHQDGSKS528 LKLGDFGLAT 538 IVDGPLYTVC548 GTPTYVAPEI558 IAETGYGLKV568 DIWAAGVITY578 ILLCGFPPFR 588 GSDQEVLFDQ600 ILMGQVDFPS610 PYWDNVSDSA620 KELITMMLLV630 DVDQRFSAVQ 640 VLEHPWVN
|
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ARG394
4.395
ILE396
3.202
GLY397
3.854
ASP398
4.984
VAL404
3.678
GLU406
3.821
ALA417
3.927
LYS419
3.149
VAL449
4.173
MET465
4.015
GLU466
3.197
LEU467
3.830
|
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| Ligand Name: Phosphonothreonine | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1-KD in complex with DCLK1-IN-1 | PDB:7KXW | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [3] |
| PDB Sequence |
IPATITERYK
391 VGRTIAVVKE406 CVERSTAREY416 ALKIIKEHMI433 QNEVSILRRV443 KHPNIVLLIE 453 EMDVPTELYL463 VMELVKGGDL473 FDAITSTNKY483 ERDASGMLYN494 LASAIKYLHS 504 LNIVHRDIKP514 ENLLVYEHSL529 KLGDFGLATI539 VDGPLYTVCG549 TPTYVAPEII 559 AETGYGLKVD569 IWAAGVITYI579 LLCGFPPFRG589 SQEVLFDQIL602 MGQVDFPSPY 612 WDNVSDSAKE622 LITMMLLVDV632 DQRFSAVQVL642 EHPWVN
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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 .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .A:482 or .A:483 or .A:485 or .A:486 or .A:487 or .A:488 or .A:489 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-ethyl-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-11-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1-Cter in complex with FMF-03-055-1 | PDB:7KX8 | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [3] |
| PDB Sequence |
IPATITERYK
391 VGRTIGDGNF401 AVVKECVERS411 TAREYALKII421 KKSKCREHMI433 QNEVSILRRV 443 KHPNIVLLIE453 EMDVPTELYL463 VMELVKGGDL473 FDYTERDASG490 MLYNLASAIK 500 YLHSLNIVHR510 DIKPENLLVY520 EKSLKLGDFG535 LATIVDGPLY545 TVCGTPTYVA 555 PEIIAETGYG565 LKVDIWAAGV575 ITYILLCGFP585 PFRGSQEVLF598 DQILMGQVDF 608 PSPYWDNVSD618 SAKELITMML628 LVDVDQRFSA638 VQVLEHPWVN648 HQLSVAGKIK 667 KHF
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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 .X8J or .X8J2 or .X8J3 or :3X8J;style chemicals stick;color identity;select .A:394 or .A:396 or .A:397 or .A:404 or .A:406 or .A:417 or .A:418 or .A:419 or .A:449 or .A:465 or .A:466 or .A:467 or .A:468 or .A:469 or .A:471 or .A:472 or .A:515 or .A:516 or .A:518 or .A:532 or .A:533; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG394
4.332
ILE396
3.513
GLY397
3.863
VAL404
3.590
GLU406
4.366
ALA417
3.599
LEU418
4.755
LYS419
3.971
VAL449
4.060
MET465
3.671
GLU466
3.559
|
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| Ligand Name: Amp Phosphoramidate | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1-KD in complex with AMPPN | PDB:5JZJ | ||||
| Method | X-ray diffraction | Resolution | 1.71 Å | Mutation | No | [2] |
| PDB Sequence |
EVSEEGFQIP
383 ATITERYKVG393 RTIGDGNFAV403 VKECVERSTA413 REYALKIIKK423 SKCRGKEHMI 433 QNEVSILRRV443 KHPNIVLLIE453 EMDVPTELYL463 VMELVKGGDL473 FDAITSTNKY 483 TERDASGMLY493 NLASAIKYLH503 SLNIVHRDIK513 PENLLVYEHQ523 DGSKSLKLGD 533 FGLATIVDGP543 LYTVCGTPTY553 VAPEIIAETG563 YGLKVDIWAA573 GVITYILLCG 583 FPPFRGSEVL597 FDQILMGQVD607 FPSPYWDNVS617 DSAKELITMM627 LLVDVDQRFS 637 AVQVLEHPWV647 N
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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 .AN2 or .AN22 or .AN23 or :3AN2;style chemicals stick;color identity;select .A:396 or .A:397 or .A:398 or .A:399 or .A:400 or .A:401 or .A:402 or .A:404 or .A:417 or .A:419 or .A:449 or .A:465 or .A:466 or .A:467 or .A:468 or .A:472 or .A:515 or .A:516 or .A:518 or .A:533; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE396
3.675
GLY397
3.604
ASP398
3.456
GLY399
3.094
ASN400
3.556
PHE401
3.428
ALA402
3.028
VAL404
3.555
ALA417
3.710
LYS419
2.649
|
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| Ligand Name: Erk5-IN-1 | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1-KD in complex with XMD8-85 | PDB:7KX6 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
QIPATITERY
390 KVGRTIGDFA402 VVKECVERST412 AREYALKIIK422 KSKHMIQNEV437 SILRRVKHPN 447 IVLLIEEMDV457 PTELYLVMEL467 VKGGDLFDAI477 TSTNKYTERD487 ASGMLYNLAS 497 AIKYLHSLNI507 VHRDIKPENL517 LVYEHQDGSK527 SLKLGDFGLA537 TIVDGPLYTV 547 CGTPTYVAPE557 IIAETGYGLK567 VDIWAAGVIT577 YILLCGFPPF587 RGSQEVLFDQ 600 ILMGQVDFPS610 PYWDNVSDSA620 KELITMMLLV630 DVDQRFSAVQ640 VLEHPWVN |
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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 .X7Y or .X7Y2 or .X7Y3 or :3X7Y;style chemicals stick;color identity;select .A:396 or .A:397 or .A:404 or .A:406 or .A:417 or .A:419 or .A:449 or .A:465 or .A:466 or .A:467 or .A:468 or .A:469 or .A:470 or .A:471 or .A:472 or .A:475 or .A:515 or .A:516 or .A:518 or .A:532 or .A:533; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE396
3.285
GLY397
3.903
VAL404
3.835
GLU406
3.395
ALA417
3.663
LYS419
4.587
VAL449
3.734
MET465
3.583
GLU466
3.315
LEU467
3.790
VAL468
2.872
|
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| Ligand Name: Dclk1-IN-1 | Ligand Info | |||||
| Structure Description | Crystal structure of DCLK1-KD in complex with DCLK1-IN-1 | PDB:7KXW | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [3] |
| PDB Sequence |
> Chain A
IPATITERYK 391 VGRTIAVVKE406 CVERSTAREY416 ALKIIKEHMI433 QNEVSILRRV443 KHPNIVLLIE 453 EMDVPTELYL463 VMELVKGGDL473 FDAITSTNKY483 ERDASGMLYN494 LASAIKYLHS 504 LNIVHRDIKP514 ENLLVYEHSL529 KLGDFGLATI539 VDGPLYTVCG549 TPTYVAPEII 559 AETGYGLKVD569 IWAAGVITYI579 LLCGFPPFRG589 SQEVLFDQIL602 MGQVDFPSPY 612 WDNVSDSAKE622 LITMMLLVDV632 DQRFSAVQVL642 EHPWVN> Chain B IPATITERYK 391 VGRTIFAVVK405 ECVERSTARE415 YALKIIKKSK425 GKEHMIQNEV437 SILRRVKHPN 447 IVLLIEEMDV457 PTELYLVMEL467 VKGGDLFDAI477 TSTNKYTERD487 ASGMLYNLAS 497 AIKYLHSLNI507 VHRDIKPENL517 LVYEHQDGSK527 SLKLGDFGLA537 TIVDGPLYTV 547 CGTPTYVAPE557 IIAETGYGLK567 VDIWAAGVIT577 YILLCGFPPF587 RGSQEVLFDQ 600 ILMGQVDFPS610 PYWDNVSDSA620 KELITMMLLV630 DVDQRFSAVQ640 VLEHPWVND |
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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 .XBD or .XBD2 or .XBD3 or :3XBD;style chemicals stick;color identity;select .A:404 or .A:417 or .A:419 or .A:449 or .A:465 or .A:466 or .A:467 or .A:468 or .A:469 or .A:471 or .A:472 or .A:475 or .A:515 or .A:516 or .A:518 or .A:532 or .A:533 or .B:396 or .B:404 or .B:406 or .B:417 or .B:418 or .B:419 or .B:449 or .B:463 or .B:465 or .B:466 or .B:467 or .B:468 or .B:469 or .B:471 or .B:472 or .B:475 or .B:515 or .B:516 or .B:517 or .B:518 or .B:532 or .B:533; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL404[A]
3.724
ALA417[A]
3.243
LYS419[A]
4.102
VAL449[A]
3.600
MET465[A]
3.630
GLU466[A]
3.296
LEU467[A]
3.863
VAL468[A]
2.561
LYS469[A]
3.710
GLY471[A]
3.736
ASP472[A]
4.216
ASP475[A]
3.012
GLU515[A]
3.729
ASN516[A]
4.015
LEU518[A]
3.516
GLY532[A]
3.917
ASP533[A]
3.719
ILE396[B]
4.161
VAL404[B]
3.242
GLU406[B]
3.732
ALA417[B]
3.204
LEU418[B]
4.962
LYS419[B]
3.953
VAL449[B]
3.494
LEU463[B]
4.923
MET465[B]
3.319
GLU466[B]
3.348
LEU467[B]
3.791
VAL468[B]
2.611
LYS469[B]
4.088
GLY471[B]
3.483
ASP472[B]
4.199
ASP475[B]
3.711
GLU515[B]
3.594
ASN516[B]
3.702
LEU517[B]
4.647
LEU518[B]
3.350
GLY532[B]
3.702
ASP533[B]
3.826
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural Basis of Inhibition of DCLK1 by Ruxolitinib. Int J Mol Sci. 2021 Aug 6;22(16):8488. | ||||
| REF 2 | Biochemical and Structural Insights into Doublecortin-like Kinase Domain 1. Structure. 2016 Sep 6;24(9):1550-61. | ||||
| REF 3 | Structural basis for small molecule targeting of Doublecortin Like Kinase 1 with DCLK1-IN-1. Commun Biol. 2021 Sep 20;4(1):1105. | ||||
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