Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T70840 | Target Info | |||
| Target Name | LIM domain kinase-1 (LIMK-1) | ||||
| Synonyms | LIMK-1; LIMK | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | LIMK1 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: AMP-PNP | Ligand Info | |||||
| Structure Description | Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP | PDB:5HVJ | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
RPHRIFRPSD
338 LIHGEVLGKG348 CFGQAIKVTH358 RETGEVMVMK368 ELIRFDEETQ378 RTFLKEVKVM 388 RCLEHPNVLK398 FIGVLYKDKR408 LNFITEYIKG418 GTLRGIIKSM428 DSQYPWSQRV 438 SFAKDIASGM448 AYLHSMNIIH458 RNLNSHNCLV468 RENKNVVVAD478 FGLARLMTVV 510 GNPYWMAPEM520 INGRSYDEKV530 DVFSFGIVLC540 EIIGRVNADP550 DYLPRTMDFG 560 LNVRGFLDRY570 CPPNCPPSFF580 PITVRCCDLD590 PEKRPSFVKL600 EHWLETLRMH 610 LAGHLPLGPQ620 LEQLDRGFWE630 TYR
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-serine-O-phosphate | Ligand Info | |||||
| Structure Description | Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 | PDB:5HVK | ||||
| Method | X-ray diffraction | Resolution | 3.50 Å | Mutation | Yes | [1] |
| PDB Sequence |
GAMGSRPHRI
333 FRPSDLIHGE343 VLGKGCFGQA353 IKVTHRETGE363 VMVMKELIRF373 DEETQRTFLK 383 EVKVMRCLEH393 PNVLKFIGVL403 YKDKRLNFIT413 EYIKGGTLRG423 IIKSMDSQYP 433 WSQRVSFAKD443 IASGMAYLHS453 MNIIHRNLNS463 HNCLVRENKN473 VVVADFGLAR 483 LMVDPDRKKR506 YVVGNPYWMA517 PEMINGRSYD527 EKVDVFSFGI537 VLCEIIGRVN 547 ADPDYLPRTM557 DFGLNVRGFL567 DRYCPPNCPP577 SFFPITVRCC587 DLDPEKRPSF 597 VKLEHWLETL607 RMHLAGHLPL617 GPQLEQLDRG627 FWETYRR
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| Ligand Name: Phosphonothreonine | Ligand Info | |||||
| Structure Description | Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1 | PDB:5HVK | ||||
| Method | X-ray diffraction | Resolution | 3.50 Å | Mutation | Yes | [1] |
| PDB Sequence |
GAMGSRPHRI
333 FRPSDLIHGE343 VLGKGCFGQA353 IKVTHRETGE363 VMVMKELIRF373 DEETQRTFLK 383 EVKVMRCLEH393 PNVLKFIGVL403 YKDKRLNFIT413 EYIKGGTLRG423 IIKSMDSQYP 433 WSQRVSFAKD443 IASGMAYLHS453 MNIIHRNLNS463 HNCLVRENKN473 VVVADFGLAR 483 LMVDPDRKKR506 YVVGNPYWMA517 PEMINGRSYD527 EKVDVFSFGI537 VLCEIIGRVN 547 ADPDYLPRTM557 DFGLNVRGFL567 DRYCPPNCPP577 SFFPITVRCC587 DLDPEKRPSF 597 VKLEHWLETL607 RMHLAGHLPL617 GPQLEQLDRG627 FWETYRR
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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:383 or .A:459 or .A:483 or .A:506 or .A:507 or .A:509 or .A:510 or .A:526; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Staurosporine | Ligand Info | |||||
| Structure Description | Crystal structure of the human LIMK1 kinase domain in complex with staurosporine | PDB:3S95 | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [2] |
| PDB Sequence |
SMPHRIFRPS
337 DLIHGEVLGK347 GCFGQAIKVT357 HRETGEVMVM367 KELIRFDEET377 QRTFLKEVKV 387 MRCLEHPNVL397 KFIGVLYKDK407 RLNFITEYIK417 GGTLRGIIKS427 MDSQYPWSQR 437 VSFAKDIASG447 MAYLHSMNII457 HRDLNSHNCL467 VRENKNVVVA477 DFGLARLMVY 507 TVVGNPYWMA517 PEMINGRSYD527 EKVDVFSFGI537 VLCEIIGRVN547 ADPDYLPRTM 557 DFGLNVRGFL567 DRYCPPNCPP577 SFFPITVRCC587 DLDPEKRPSF597 VKLEHWLETL 607 RMHLAGHLPL617 GPQLEQLDRG627 FWETYRRGES637
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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 .STU or .STU2 or .STU3 or :3STU;style chemicals stick;color identity;select .A:345 or .A:346 or .A:347 or .A:353 or .A:366 or .A:368 or .A:384 or .A:397 or .A:411 or .A:413 or .A:414 or .A:415 or .A:416 or .A:417 or .A:419 or .A:420 or .A:464 or .A:465 or .A:467 or .A:477 or .A:478; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU345
3.584
GLY346
3.419
LYS347
4.745
ALA353
3.853
VAL366
3.512
LYS368
3.133
GLU384
3.170
LEU397
3.680
PHE411
4.815
THR413
3.226
GLU414
2.847
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| Ligand Name: PF-477736 | Ligand Info | |||||
| Structure Description | LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736 | PDB:5NXC | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [3] |
| PDB Sequence |
SMPHRIFRPS
337 DLIHGEVLGK347 GCFGQAIKVT357 HRETGEVMVM367 KELIRFDEET377 QRTFLKEVKV 387 MRCLEHPNVL397 KFIGVLYKDK407 RLNFITEYIK417 GGTLRGIIKS427 MDSQYPWSQR 437 VSFAKDIASG447 MAYLHSMNII457 HRDLNSHNCL467 VRENKNVVVA477 DFGNPYWMAP 518 EMINGRSYDE528 KVDVFSFGIV538 LCEIIGRVNA548 DPDYLPRTMD558 FGLNVRGFLD 568 RYCPPNCPPS578 FFPITVRCCD588 LDPEKRPSFV598 KLEHWLETLR608 MHLAGHLPLG 618 PQLEQLDRGF628 WETY
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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 .9DB or .9DB2 or .9DB3 or :39DB;style chemicals stick;color identity;select .L:345 or .L:346 or .L:347 or .L:348 or .L:350 or .L:351 or .L:352 or .L:353 or .L:366 or .L:368 or .L:369 or .L:370 or .L:397 or .L:413 or .L:414 or .L:415 or .L:416 or .L:417 or .L:418 or .L:419 or .L:420 or .L:464 or .L:467 or .L:477 or .L:478; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU345
3.824
GLY346
3.454
LYS347
3.205
GLY348
3.947
PHE350
3.719
GLY351
3.340
GLN352
3.362
ALA353
3.725
VAL366
3.479
LYS368
2.622
GLU369
4.754
LEU370
4.662
LEU397
3.201
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| Ligand Name: N-(5-(1-(2,6-dichlorophenyl)-3-(difluoromethyl)-1H-pyrazol-5-yl)thiazol-2-yl)isobutyramide | Ligand Info | |||||
| Structure Description | LIM Domain Kinase 1 (LIMK1) bound to LIMKi3 | PDB:8AAU | ||||
| Method | X-ray diffraction | Resolution | 1.74 Å | Mutation | No | [4] |
| PDB Sequence |
SMPHRIFRPS
337 DLIHGEVLGK347 GCFGQAIKVT357 HRETGEVMVM367 KELIRFDEET377 QRTFLKEVKV 387 MRCLEHPNVL397 KFIGVLYKDK407 RLNFITEYIK417 GGTLRGIIKS427 MDSQYPWSQR 437 VSFAKDIASG447 MAYLHSMNII457 HRDLNSHNCL467 VRENKNVVVA477 DFGLARLMDR 503 KKRYTVVGNP513 YWMAPEMING523 RSYDEKVDVF533 SFGIVLCEII543 GRVNADPDYL 553 PRTMDFGLNV563 RGFLDRYCPP573 NCPPSFFPIT583 VRCCDLDPEK593 RPSFVKLEHW 603 LETLRMHLAG613 HLPLGPQLEQ623 LDRGFWETYR633 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 .LH0 or .LH02 or .LH03 or :3LH0;style chemicals stick;color identity;select .L:345 or .L:346 or .L:353 or .L:366 or .L:367 or .L:368 or .L:384 or .L:388 or .L:397 or .L:411 or .L:413 or .L:414 or .L:415 or .L:416 or .L:417 or .L:418 or .L:419 or .L:420 or .L:464 or .L:465 or .L:467 or .L:477 or .L:478; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU345
3.467
GLY346
3.724
ALA353
3.446
VAL366
3.607
MET367
4.852
LYS368
3.612
GLU384
4.301
MET388
4.317
LEU397
3.859
PHE411
3.727
THR413
3.423
GLU414
3.579
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| Ligand Name: Phosphothiophosphoric acid-adenylate ester | Ligand Info | |||||
| Structure Description | Structure Of the LIMK1-ATPgammaS-CFL1 Complex | PDB:5L6W | ||||
| Method | X-ray diffraction | Resolution | 2.53 Å | Mutation | Yes | [5] |
| PDB Sequence |
SMPHRIFRPS
337 DLIHGEVLGK347 GCFGQAIKVT357 HRETGEVMVM367 KELIRFDEET377 QRTFLKEVKV 387 MRCLEHPNVL397 KFIGVLYKDK407 RLNFITEYIK417 GGTLRGIIKS427 MDSQYPWSQR 437 VSFAKDIASG447 MAYLHSMNII457 HRDLNSHNCL467 VRENKNVVVA477 DFGLARLMDR 503 KKRYTVVGNP513 YWMAPEMING523 RSYDEKVDVF533 SFGIVLCEII543 GRVNADPDYL 553 PRTMDFGLNV563 RGFLDRYCPP573 NCPPSFFPIT583 VRCCDLDPEK593 RPSFVKLEHW 603 LETLRMHLAG613 HLPLGPQLEQ623 LDRGFWETYR633
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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 .AGS or .AGS2 or .AGS3 or :3AGS;style chemicals stick;color identity;select .L:345 or .L:346 or .L:353 or .L:366 or .L:368 or .L:397 or .L:413 or .L:414 or .L:415 or .L:416 or .L:419 or .L:420 or .L:460 or .L:464 or .L:465 or .L:467 or .L:478 or .L:480 or .L:481; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide | Ligand Info | |||||
| Structure Description | The LIMK1 Kinase Domain Bound To LIJTF500025 | PDB:7ATU | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [6] |
| PDB Sequence |
MPHRIFGEVL
345 GKGCFGQAIK355 VTHRETGEVM365 VMKELIRFDE375 ETQRTFLKEV385 KVMRCLEHPN 395 VLKFIGVLYK407 RLNFITEYIK417 GGTLRGIIKS427 MDSQYPWSQR437 VSFAKDIASG 447 MAYLHSMNII457 HRDLNSHNCL467 VRENKNVVVA477 DFGLARLMYT508 VVGNPYWMAP 518 EMINGRSYDE528 KVDVFSFGIV538 LCEIIGRVNA548 DPDYLPRTMD558 FGLNVRGFLD 568 RYCPPNCPPS578 FFPITVRCCD588 LDPEKRPSFV598 KLEHWLETLR608 MHLAGHLPLG 618 PQLEQLDRGF628 WETYRR
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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 .RXN or .RXN2 or .RXN3 or :3RXN;style chemicals stick;color identity;select .A:347 or .A:350 or .A:351 or .A:352 or .A:353 or .A:366 or .A:367 or .A:368 or .A:370 or .A:388 or .A:391 or .A:396 or .A:397 or .A:398 or .A:399 or .A:411 or .A:412 or .A:413 or .A:451 or .A:456 or .A:458 or .A:476 or .A:477 or .A:478 or .A:479 or .A:480 or .A:481 or .A:483; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS347
4.017
PHE350
3.451
GLY351
4.562
GLN352
4.133
ALA353
3.372
VAL366
3.020
MET367
4.085
LYS368
3.269
LEU370
4.783
MET388
3.209
LEU391
3.791
VAL396
3.509
LEU397
2.472
LYS398
3.908
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| Ligand Name: 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide | Ligand Info | |||||
| Structure Description | Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 | PDB:7B8W | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [7] |
| PDB Sequence |
PHRIFRPSDL
339 IHGEVLGKGC349 FGQAIKVTHR359 ETGEVMVMKE369 LIRFDEETQR379 TFLKEVKVMR 389 CLEHPNVLKF399 IGVLYKDKRL409 NFITEYIKGG419 TLRGIIKSMD429 SQYPWSQRVS 439 FAKDIASGMA449 YLHSMNIIHR459 DLNSHNCLVR469 ENKNVVVADF479 GLARLMVNPY 514 WMAPEMINGR524 SYDEKVDVFS534 FGIVLCEIIG544 RVNADPDYLP554 RTMDFGLNVR 564 GFLDRYCPPN574 CPPSFFPITV584 RCCDLDPEKR594 PSFVKLEHWL604 ETLRMHLAGH 614 LPLGPQLEQL624 DRGFWETYR
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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 .T3B or .T3B2 or .T3B3 or :3T3B;style chemicals stick;color identity;select .A:345 or .A:350 or .A:353 or .A:366 or .A:368 or .A:369 or .A:370 or .A:373 or .A:388 or .A:391 or .A:396 or .A:397 or .A:399 or .A:411 or .A:413 or .A:414 or .A:415 or .A:416 or .A:417 or .A:418 or .A:419 or .A:420 or .A:451 or .A:456 or .A:458 or .A:467 or .A:476 or .A:477 or .A:478 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU345
3.990
PHE350
4.498
ALA353
4.795
VAL366
3.601
LYS368
3.340
GLU369
3.649
LEU370
3.342
PHE373
4.857
MET388
2.906
LEU391
3.700
VAL396
3.438
LEU397
3.402
PHE399
3.719
PHE411
3.734
THR413
3.157
GLU414
3.571
TYR415
3.624
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| Ligand Name: N-[3-[5-(4-Chlorophenyl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl]benzenesulfonamide | Ligand Info | |||||
| Structure Description | The LIMK1 Kinase Domain Bound To LIJTF500127 | PDB:7ATS | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [8] |
| PDB Sequence |
SMPHRIFRPS
337 DLIHGEVLGK347 GCFGQAIKVT357 HRETGEVMVM367 KELIRFDEET377 QRTFLKEVKV 387 MRCLEHPNVL397 KFIGVLYKDK407 RLNFITEYIK417 GGTLRGIIKS427 MDSQYPWSQR 437 VSFAKDIASG447 MAYLHSMNII457 HRDLNSHNCL467 VRENKNVVVA477 DFGPYWMAPE 519 MINGRSYDEK529 VDVFSFGIVL539 CEIIGRVNAD549 PDYLPRTMDF559 GLNVRGFLDR 569 YCPPNCPPSF579 FPITVRCCDL589 DPEKRPSFVK599 LEHWLETLRM609 HLAGHLPLGP 619 QLEQLDRGFW629 ETYRR
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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 .RXQ or .RXQ2 or .RXQ3 or :3RXQ;style chemicals stick;color identity;select .A:345 or .A:353 or .A:366 or .A:367 or .A:368 or .A:388 or .A:396 or .A:397 or .A:398 or .A:399 or .A:411 or .A:413 or .A:414 or .A:415 or .A:416 or .A:419 or .A:420 or .A:467 or .A:476 or .A:477 or .A:478 or .A:479 or .A:480; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU345
3.600
ALA353
3.780
VAL366
2.966
MET367
4.397
LYS368
3.638
MET388
3.461
VAL396
4.532
LEU397
3.368
LYS398
4.789
PHE399
4.103
PHE411
3.527
THR413
3.164
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. Mol Cell. 2016 May 5;62(3):397-408. | ||||
| REF 2 | Crystal structure of the human LIMK1 kinase domain in complex with staurosporine | ||||
| REF 3 | LIM Domain Kinase (LIMK1) In Complex With PF-00477736 | ||||
| REF 4 | Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes. J Med Chem. 2022 Oct 13;65(19):13264-13287. | ||||
| REF 5 | Structure Of the LIMK1-ATPgammaS-CFL1 Complex | ||||
| REF 6 | The LIMK1 Kinase Domain Bound To LIJTF500025 | ||||
| REF 7 | Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 | ||||
| REF 8 | The LIMK1 Kinase Domain Bound To LIJTF500127 | ||||
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