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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1yi4ADNSerine/threonine-protein kinase pim-12.7.11.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1yi4ADNSerine/threonine-protein kinase pim-12.7.11.11.000
3cy3JN5Serine/threonine-protein kinase pim-12.7.11.10.700
3c4eC4ESerine/threonine-protein kinase pim-12.7.11.10.657
2bilBI1Serine/threonine-protein kinase pim-12.7.11.10.640
2o65MYFSerine/threonine-protein kinase pim-12.7.11.10.639
2j2iLY4Serine/threonine-protein kinase pim-12.7.11.10.631
1yhsSTUSerine/threonine-protein kinase pim-12.7.11.10.626
2objVRVSerine/threonine-protein kinase pim-12.7.11.10.624
3bgqVX2Serine/threonine-protein kinase pim-12.7.11.10.617
3uixQ17Serine/threonine-protein kinase pim-12.7.11.10.617
4k0y1OASerine/threonine-protein kinase pim-12.7.11.10.616
3jxwLXGSerine/threonine-protein kinase pim-12.7.11.10.613
3bgzVX3Serine/threonine-protein kinase pim-12.7.11.10.609
3jpv1DRSerine/threonine-protein kinase pim-12.7.11.10.609
4lm5Q17Serine/threonine-protein kinase pim-12.7.11.10.606
4lmuQUESerine/threonine-protein kinase pim-12.7.11.10.604
5dgzL20Serine/threonine-protein kinase pim-12.7.11.10.601
1yi3LY2Serine/threonine-protein kinase pim-12.7.11.10.597
4dtk7LISerine/threonine-protein kinase pim-12.7.11.10.597
4k181OBSerine/threonine-protein kinase pim-12.7.11.10.597
1xwsBI1Serine/threonine-protein kinase pim-12.7.11.10.595
3umxQ18Serine/threonine-protein kinase pim-12.7.11.10.595
3bgpVX1Serine/threonine-protein kinase pim-12.7.11.10.587
3cy2MB9Serine/threonine-protein kinase pim-12.7.11.10.587
4a7cE46Serine/threonine-protein kinase pim-12.7.11.10.585
3ma301ISerine/threonine-protein kinase pim-12.7.11.10.584
3r02UNMSerine/threonine-protein kinase pim-12.7.11.10.582
4mbl26LSerine/threonine-protein kinase pim-12.7.11.10.574
4n702HXSerine/threonine-protein kinase pim-12.7.11.10.568
3dcv55ESerine/threonine-protein kinase pim-12.7.11.10.567
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.567
4gw83RASerine/threonine-protein kinase pim-12.7.11.10.564
4k1b1OCSerine/threonine-protein kinase pim-12.7.11.10.564
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.563
3vbq0F5Serine/threonine-protein kinase pim-12.7.11.10.560
2xizXIZSerine/threonine-protein kinase pim-12.7.11.10.559
3jy0LYGSerine/threonine-protein kinase pim-12.7.11.10.558
2bikBI1Serine/threonine-protein kinase pim-12.7.11.10.550
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.547
2c3iIYZSerine/threonine-protein kinase pim-12.7.11.10.545
3cxw7CPSerine/threonine-protein kinase pim-12.7.11.10.542
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.541
3iw4LW4Protein kinase C alpha type2.7.11.130.540
2xiyXIYSerine/threonine-protein kinase pim-12.7.11.10.538
4n6z2HWSerine/threonine-protein kinase pim-12.7.11.10.531
4i41MIXSerine/threonine-protein kinase pim-12.7.11.10.527
2jedLG8Protein kinase C theta type2.7.11.130.525
4enxZ20Serine/threonine-protein kinase pim-12.7.11.10.524
4enyJ19Serine/threonine-protein kinase pim-12.7.11.10.517
3qf9NM8Serine/threonine-protein kinase pim-12.7.11.10.515
3umw596Serine/threonine-protein kinase pim-12.7.11.10.515
4othDRNSerine/threonine-protein kinase N1/0.514
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.509
2xj1XJ1Serine/threonine-protein kinase pim-12.7.11.10.504
4bgg844Activin receptor type-12.7.11.300.503
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.499
4i22IREEpidermal growth factor receptor2.7.10.10.498
3a4pDFQHepatocyte growth factor receptor2.7.10.10.497
1xr1ANPSerine/threonine-protein kinase pim-12.7.11.10.496
4acc7YGGlycogen synthase kinase-3 beta2.7.11.260.495
4acg6LQGlycogen synthase kinase-3 beta2.7.11.260.492
4dymIYZActivin receptor type-12.7.11.300.490
2xj2985Serine/threonine-protein kinase pim-12.7.11.10.489
4hyi1AOSerine/threonine-protein kinase Chk12.7.11.10.489
3u9n09HSerine/threonine-protein kinase Chk12.7.11.10.488
3mtfA3FActivin receptor type-12.7.11.300.487
2ckeIQUDeath-associated protein kinase 2/0.485
4fg7ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.485
4jq8KJ8Epidermal growth factor receptor2.7.10.10.484
5av2KMPDeath-associated protein kinase 12.7.11.10.484
3l1sZ92Glycogen synthase kinase-3 beta2.7.11.260.483
4hni16WCasein kinase I isoform epsilon2.7.11.10.483
4bchT7ZCyclin-dependent kinase 92.7.11.220.481
4hnf16WCasein kinase I isoform delta2.7.11.10.481
3sayOFTGlycogen synthase kinase-3 beta2.7.11.260.480
4acdGR9Glycogen synthase kinase-3 beta2.7.11.260.480
4gmy0X5Tyrosine-protein kinase JAK2/0.480
2itpAEEEpidermal growth factor receptor2.7.10.10.479
3uyt0CKCasein kinase I isoform delta2.7.11.10.477
2ydjYDJSerine/threonine-protein kinase Chk12.7.11.10.476
3pjcPJCTyrosine-protein kinase JAK32.7.10.20.476
4yuqKS1Calmodulin-like domain protein kinase/0.475
1xjdSTUProtein kinase C theta type2.7.11.130.474
2uxpCLMHTH-type transcriptional regulator TtgR/0.473
3oom507Activin receptor type-12.7.11.300.473
1zys199Serine/threonine-protein kinase Chk12.7.11.10.472
4afjSJJGlycogen synthase kinase-3 beta2.7.11.260.472
1h1s4SPCyclin-dependent kinase 22.7.11.220.471
4wboANWRhodopsin kinase/0.468
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.468
1stcSTUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.467
2broDF2Serine/threonine-protein kinase Chk12.7.11.10.467
4ks8B49Serine/threonine-protein kinase PAK 62.7.11.10.467
1aq1STUCyclin-dependent kinase 22.7.11.220.466
4b7tCWTGlycogen synthase kinase-3 beta2.7.11.260.466
3f883HTGlycogen synthase kinase-3 beta2.7.11.260.465
3vs5VSGTyrosine-protein kinase HCK2.7.10.20.465
3mvl38PMitogen-activated protein kinase 14/0.464
4achKDIGlycogen synthase kinase-3 beta2.7.11.260.464
1wvxBD4Death-associated protein kinase 12.7.11.10.463
3du8553Glycogen synthase kinase-3 beta2.7.11.260.462
3vrzVRZTyrosine-protein kinase HCK2.7.10.20.462
4gg70J8Hepatocyte growth factor receptor2.7.10.10.462
3dtcVINMitogen-activated protein kinase kinase kinase 92.7.11.250.461
3sd0TSKGlycogen synthase kinase-3 beta2.7.11.260.461
3vs7KS1Tyrosine-protein kinase HCK2.7.10.20.461
4bbe3O4Tyrosine-protein kinase JAK2/0.461
3gu6ADPDeath-associated protein kinase 12.7.11.10.460
3t8oATPRhodopsin kinase/0.460
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.459
2ittAEEEpidermal growth factor receptor2.7.10.10.459
3gubGUBDeath-associated protein kinase 12.7.11.10.458
4grb0XGCasein kinase II subunit alpha2.7.11.10.458
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.457
4fob0USALK tyrosine kinase receptor2.7.10.10.457
5auwQUEDeath-associated protein kinase 12.7.11.10.457
4kikKSAInhibitor of nuclear factor kappa-B kinase subunit beta2.7.11.100.456
3zh8C58Protein kinase C iota type2.7.11.130.455
4ftjH8KSerine/threonine-protein kinase Chk12.7.11.10.455
3vs2VSBTyrosine-protein kinase HCK2.7.10.20.454
4aojV4ZHigh affinity nerve growth factor receptor2.7.10.10.454
4bibIEOMitogen-activated protein kinase kinase kinase 52.7.11.250.454
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.454
4fnyI3KALK tyrosine kinase receptor2.7.10.10.454
4ic7ANPMitogen-activated protein kinase 72.7.11.240.454
5av3KMPDeath-associated protein kinase 12.7.11.10.454
2brmDFZSerine/threonine-protein kinase Chk12.7.11.10.453
4feq0T8Tyrosine-protein kinase receptor TYRO32.7.10.10.453
4kbk1QGCasein kinase I isoform delta2.7.11.10.453
3gc9B45Mitogen-activated protein kinase 112.7.11.240.452
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.452
5f0a1FBcGMP-dependent protein kinase, putative/0.452
1eh4IC1Casein kinase I homolog 12.7.11.10.451
3t9i3T9Serine/threonine-protein kinase pim-12.7.11.10.451
4bdfH3RSerine/threonine-protein kinase Chk22.7.11.10.451
4bfmANPMaternal embryonic leucine zipper kinase2.7.11.10.451
4c02TAKActivin receptor type-12.7.11.300.451
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.451
1q4t4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.450
1u4dDBQActivated CDC42 kinase 1/0.450
2br1PFPSerine/threonine-protein kinase Chk12.7.11.10.450
2h8hH8HProto-oncogene tyrosine-protein kinase Src2.7.10.20.450
3bu5ATPInsulin receptor2.7.10.10.450
3c7qXINVascular endothelial growth factor receptor 22.7.10.10.450
3sheI85MAP kinase-activated protein kinase 32.7.11.10.450
4dgnLU2Casein kinase II subunit alpha2.7.11.10.450
4jr3KJREpidermal growth factor receptor2.7.10.10.450
4oacADPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.450
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.449
2uxuNARHTH-type transcriptional regulator TtgR/0.449
2yirYIRSerine/threonine-protein kinase Chk22.7.11.10.449
3bhtMFRCyclin-dependent kinase 22.7.11.220.449
3kc3MK2MAP kinase-activated protein kinase 22.7.11.10.449
3vs4VSFTyrosine-protein kinase HCK2.7.10.20.449
4aacAAVMitogen-activated protein kinase 14/0.449
4k110J9Proto-oncogene tyrosine-protein kinase Src2.7.10.20.449
5auxKMPDeath-associated protein kinase 12.7.11.10.449
2hog710Serine/threonine-protein kinase Chk12.7.11.10.448
2ym6YM6Serine/threonine-protein kinase Chk12.7.11.10.448
3w33W19Epidermal growth factor receptor2.7.10.10.448
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2xbjXBJSerine/threonine-protein kinase Chk22.7.11.10.447
3a60STURibosomal protein S6 kinase beta-12.7.11.10.447
3ormAGSSerine/threonine protein kinase/0.447
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.447
4jq7KJQEpidermal growth factor receptor2.7.10.10.447
4qmzB49Serine/threonine-protein kinase 242.7.11.10.447
3bqr4RBDeath-associated protein kinase 3/0.446
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
3w2sW2REpidermal growth factor receptor2.7.10.10.446
2hy0306Serine/threonine-protein kinase Chk12.7.11.10.445
3blrCPBCyclin-dependent kinase 92.7.11.220.445
3vetADPnebramycin 5' synthase6.1.2.20.445
4a06ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.445
4g170VNCasein kinase I isoform gamma-32.7.11.10.445
4ib4ERM5-hydroxytryptamine receptor 2B/0.445
5auuLU2Death-associated protein kinase 12.7.11.10.445
5auvAGIDeath-associated protein kinase 12.7.11.10.445
1qcfPP1Tyrosine-protein kinase HCK2.7.10.20.444
2j0k4STFocal adhesion kinase 12.7.10.20.444
3r3b4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.444
4bidIE8Mitogen-activated protein kinase kinase kinase 52.7.11.250.444
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.443
2gcdSTUSerine/threonine-protein kinase TAO22.7.11.10.443
3a4oSTUTyrosine-protein kinase Lyn2.7.10.20.443
3c4xATPRhodopsin kinase/0.443
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4xlvACPInsulin receptor2.7.10.10.443
1nvrSTUSerine/threonine-protein kinase Chk12.7.11.10.442
1t1rIMB1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.442
2acxANPG protein-coupled receptor kinase 62.7.11.160.442
2ycqUPXSerine/threonine-protein kinase Chk22.7.11.10.442
3hllI45Mitogen-activated protein kinase 14/0.442
1p4fDRGDeath-associated protein kinase 12.7.11.10.441
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.441
2i0ePDSProtein kinase C beta type2.7.11.130.441
2xk9XK9Serine/threonine-protein kinase Chk22.7.11.10.441
2ycsNXPSerine/threonine-protein kinase Chk22.7.11.10.441
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
3kn5ANPRibosomal protein S6 kinase alpha-52.7.11.10.441
4fkg4CKCyclin-dependent kinase 22.7.11.220.441
4fr4STUSerine/threonine-protein kinase 32A2.7.11.10.441
1k7fIAVTryptophan synthase alpha chain/0.440
1m17AQ4Epidermal growth factor receptor2.7.10.10.440
1q1rFADPutidaredoxin reductase1.18.1.50.440
3l9nL9NcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.440