Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T09133 Target Info
Target Name LIM domain kinase-2 (LIMK-2)
Synonyms LIMK-2; LIM domain kinase 2
Target Type Literature-reported Target
Gene Name LIMK2
Biochemical Class Kinase
UniProt ID
LIMK2_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide Ligand Info
Structure Description LIM domain kinase 2 (LIMK2) in complex with TH-470 PDB:7QHG
Method X-ray diffraction Resolution 1.45 Å Mutation No [1]
PDB Sequence
MDLIHGEVLG
338
KGFFGQAIKV
348
THKATGKVMV
358
MKELIRCDEE
368
TQKTFLTEVK
378

VMRSLDHPNV
388
LKFIGVLYKD
398
KKLNLLTEYI
408
EGGTLKDFLR
418
SMDPFPWQQK
428

VRFAKGIASG
438
MAYLHSMCII
448
HRDLNSHNCL
458
IKLDKTVVVA
468
DFGLSRLIVD
499

RKKRYTVVGN
509
PYWMAPEMLN
519
GKSYDETVDI
529
FSFGIVLCEI
539
IGQVYADPDC
549

LPRTLDFGLN
559
VKLFWEKFVP
569
TDCPPAFFPL
579
AAICCRLEPE
589
SRPAFSKLED
599

SFEALSLYLG
609
ELGIPLPAEL
619
EELDHTVSMQ
629
YGL
Residue
Distance (Å)
LEU337
3.732
PHE342
4.918
VAL358
3.572
LYS360
3.518
GLU361
3.831
LEU362
4.208
MET380
3.115
LEU383
3.290
VAL388
3.589
LEU389
3.411
PHE391
3.390
LEU403
3.574
THR405
3.079
GLU406
3.364
TYR407
3.932
ILE408
2.773
Residue
Distance (Å)
GLU409
4.566
GLY410
3.726
GLY411
3.508
THR412
4.161
LEU442
3.732
ILE447
4.556
HIS449
3.663
LEU458
3.726
ILE459
4.674
VAL467
3.403
ALA468
3.480
ASP469
2.932
PHE470
3.165
GLY471
4.407
LEU472
3.650
ARG474
2.933
Ligand Name: 4-[(3-Chlorophenyl)sulfamoyl]-~{n}-(Phenylmethyl)-~{n}-Propyl-Benzamide Ligand Info
Structure Description LIM Domain Kinase 2 (LIMK2) In Complex With TH-300 PDB:5NXD
Method X-ray diffraction Resolution 1.90 Å Mutation No [2]
PDB Sequence
DLIHGEVLGK
339
GFFGQAIKVT
349
HKATGKVMVM
359
KELIRCDEET
369
QKTFLTEVKV
379

MRSLDHPNVL
389
KFIGVLYKDK
399
KLNLLTEYIE
409
GGTLKDFLRS
419
MDPFPWQQKV
429

RFAKGIASGM
439
AYLHSMCIIH
449
RDLNSHNCLI
459
KLDKTVVVAD
469
FGLSRLIVPY
511

WMAPEMLNGK
521
SYDETVDIFS
531
FGIVLCEIIG
541
QVYADPDCLP
551
RTLDFGLNVK
561

LFWEKFVPTD
571
CPPAFFPLAA
581
ICCRLEPESR
591
PAFSKLEDSF
601
EALSLYLGEL
611

GIPLPAELEE
621
LDHTVSMQYG
631
L
Residue
Distance (Å)
LEU337
4.644
ALA345
4.462
VAL358
4.016
LYS360
3.546
GLU361
3.588
LEU362
4.217
MET380
3.179
LEU383
3.548
VAL388
3.549
LEU389
3.569
PHE391
3.274
LEU403
3.686
Residue
Distance (Å)
THR405
3.671
LEU442
3.690
ILE447
4.009
ILE448
4.903
HIS449
3.489
VAL467
3.341
ALA468
3.573
ASP469
2.941
PHE470
3.254
GLY471
4.439
LEU472
3.448
ARG474
2.961
Ligand Name: N-{4-[(1s)-1,2-Dihydroxyethyl]benzyl}-N-Methyl-4-(Phenylsulfamoyl)benzamide Ligand Info
Structure Description Crystal Structure of the Human LIMK2 Kinase Domain In Complex With a Non-ATP Competitive Inhibitor PDB:4TPT
Method X-ray diffraction Resolution 2.60 Å Mutation No [3]
PDB Sequence
DLIHGEVLGK
339
GFFGQAIKVT
349
HKATGKVMVM
359
KELIRCDEET
369
QKTFLTEVKV
379

MRSLDHPNVL
389
KFIGVLYKDK
399
KLNLLTEYIE
409
GGTLKDFLRS
419
MDPFPWQQKV
429

RFAKGIASGM
439
AYLHSMCIIH
449
RDLNSHNCLI
459
KLDKTVVVAD
469
FGLSRLIVKK
502

RYTVVGNPYW
512
MAPEMLNGKS
522
YDETVDIFSF
532
GIVLCEIIGQ
542
VYADPDCLPR
552

TLDFGLNVKL
562
FWEKFVPTDC
572
PPAFFPLAAI
582
CCRLEPESRP
592
AFSKLEDSFE
602

ALSLYLGELG
612
IPLPAELEEL
622
DHTVSMQYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .35H or .35H2 or .35H3 or :335H;style chemicals stick;color identity;select .A:342 or .A:360 or .A:361 or .A:362 or .A:363 or .A:364 or .A:380 or .A:383 or .A:388 or .A:389 or .A:391 or .A:403 or .A:405 or .A:442 or .A:447 or .A:449 or .A:467 or .A:468 or .A:469 or .A:470 or .A:471 or .A:472 or .A:474; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE342
4.425
LYS360
3.702
GLU361
3.455
LEU362
3.965
ILE363
2.976
ARG364
4.377
MET380
3.122
LEU383
3.317
VAL388
3.596
LEU389
3.347
PHE391
3.477
LEU403
3.757
Residue
Distance (Å)
THR405
3.362
LEU442
3.821
ILE447
4.583
HIS449
3.801
VAL467
3.340
ALA468
3.582
ASP469
3.044
PHE470
3.137
GLY471
4.575
LEU472
3.627
ARG474
3.136
References  Top
REF 1 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 2 LIM Domain Kinase 2 (LIMK2)In Complex With TH-300
REF 3 Discovery of a Type III Inhibitor of LIM Kinase 2 That Binds in a DFG-Out Conformation. ACS Med Chem Lett. 2014 Aug 7;6(1):53-7

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