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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
2pmnK51Protein kinase 7

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2pmnK51Protein kinase 7/1.000
2pmlANPUncharacterized protein/0.549
4u97STUInterleukin-1 receptor-associated kinase 42.7.11.10.532
2pmoHMDProtein kinase 7/0.531
3rmf20ZCyclin-dependent kinase 22.7.11.220.513
3qrtX14Cyclin-dependent kinase 22.7.11.220.508
3ql8X01Cyclin-dependent kinase 22.7.11.220.504
2fznFADBifunctional protein PutA1.5.5.20.502
4acm7YGCyclin-dependent kinase 22.7.11.220.499
1tj0FADBifunctional protein PutA1.5.5.20.498
1h1pCMGCyclin-dependent kinase 22.7.11.220.497
2b52D42Cyclin-dependent kinase 22.7.11.220.497
4eok4SPCyclin-dependent kinase 22.7.11.220.497
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.495
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.493
3r9dX6BCyclin-dependent kinase 22.7.11.220.493
2y9qANPMitogen-activated protein kinase 12.7.11.240.492
1oi9N20Cyclin-dependent kinase 22.7.11.220.488
3qqkX02Cyclin-dependent kinase 22.7.11.220.487
3ral04ZCyclin-dependent kinase 22.7.11.220.486
3sqq99ZCyclin-dependent kinase 22.7.11.220.485
4bchT7ZCyclin-dependent kinase 92.7.11.220.485
3rak03ZCyclin-dependent kinase 22.7.11.220.484
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.483
2gcdSTUSerine/threonine-protein kinase TAO22.7.11.10.483
3w32W32Epidermal growth factor receptor2.7.10.10.483
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.481
1e9hINRCyclin-dependent kinase 22.7.11.220.480
3pxyJWSCyclin-dependent kinase 22.7.11.220.480
4qnaX11Serine/threonine-protein kinase 242.7.11.10.479
3rm618ZCyclin-dependent kinase 22.7.11.220.478
3u9n09HSerine/threonine-protein kinase Chk12.7.11.10.478
2r0uM54Serine/threonine-protein kinase Chk12.7.11.10.477
4bdfH3RSerine/threonine-protein kinase Chk22.7.11.10.477
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.476
2iw6QQ2Cyclin-dependent kinase 22.7.11.220.475
1nzfUPGDNA beta-glucosyltransferase/0.474
1u59STUTyrosine-protein kinase ZAP-702.7.10.20.474
2hog710Serine/threonine-protein kinase Chk12.7.11.10.474
2wotZZGTGF-beta receptor type-12.7.11.300.474
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.474
1oiyN41Cyclin-dependent kinase 22.7.11.220.472
2j9gANPBiotin carboxylase6.3.4.140.471
3nup3NUCyclin-dependent kinase 62.7.11.220.471
4fmqANPMitogen-activated protein kinase 12.7.11.240.471
2brhDFWSerine/threonine-protein kinase Chk12.7.11.10.470
3hdmMMGSerine/threonine-protein kinase Sgk12.7.11.10.470
3lfqA28Cyclin-dependent kinase 22.7.11.220.470
2br1PFPSerine/threonine-protein kinase Chk12.7.11.10.469
4o8aFADBifunctional protein PutA1.2.1.880.469
3s0o50ZCyclin-dependent kinase 22.7.11.220.468
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.468
4dit0KDGlycogen synthase kinase-3 beta2.7.11.260.468
2r64740Cyclin-dependent kinase 22.7.11.220.467
3c13EMOCasein kinase II subunit alpha2.7.11.10.467
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.466
2i40BLZCyclin-dependent kinase 22.7.11.220.466
2wtcVGMSerine/threonine-protein kinase Chk22.7.11.10.466
1oiuN76Cyclin-dependent kinase 22.7.11.220.465
1pkdUCNCyclin-dependent kinase 22.7.11.220.465
4fic0ULProto-oncogene tyrosine-protein kinase Src2.7.10.20.465
2objVRVSerine/threonine-protein kinase pim-12.7.11.10.464
3ibqATPPyridoxal kinase/0.464
3o0g3O0Cyclin-dependent-like kinase 52.7.11.10.464
1v0oINRCell division control protein 2 homolog2.7.11.220.463
3uyt0CKCasein kinase I isoform delta2.7.11.10.463
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.463
4ej4EJ4Delta-type opioid receptor/0.463
1nvrSTUSerine/threonine-protein kinase Chk12.7.11.10.462
1v1k3FPCyclin-dependent kinase 22.7.11.220.462
4fszHK8Serine/threonine-protein kinase Chk12.7.11.10.462
2w0jZATSerine/threonine-protein kinase Chk22.7.11.10.461
3b7dCNIGlutamate receptor 2/0.461
3iafTPPBenzaldehyde lyase/0.461
3rni21ZCyclin-dependent kinase 22.7.11.220.461
3vjoANPEpidermal growth factor receptor2.7.10.10.461
3w33W19Epidermal growth factor receptor2.7.10.10.461
4b99R4LMitogen-activated protein kinase 72.7.11.240.461
4ftu7HKSerine/threonine-protein kinase Chk12.7.11.10.461
4i22IREEpidermal growth factor receptor2.7.10.10.461
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.461
2ds11CDCyclin-dependent kinase 22.7.11.220.460
3t3c017Gag-Pol polyprotein3.4.23.160.460
4n6hEJ4Delta-type opioid receptor/0.460
1h1s4SPCyclin-dependent kinase 22.7.11.220.459
1vyw292Cyclin-dependent kinase 22.7.11.220.459
2btsU32Cyclin-dependent kinase 22.7.11.220.459
2f2cAP9Cyclin-dependent kinase 62.7.11.220.459
3rk708ZCyclin-dependent kinase 22.7.11.220.459
1di8DTQCyclin-dependent kinase 22.7.11.220.458
1tj1FADBifunctional protein PutA1.5.5.20.458
2brmDFZSerine/threonine-protein kinase Chk12.7.11.10.458
2qhm7CSSerine/threonine-protein kinase Chk12.7.11.10.458
3bkbSTUTyrosine-protein kinase Fes/Fps2.7.10.20.458
3mfrANPPeripheral plasma membrane protein CASK2.7.11.10.458
4c34STUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
4gk3L87Ephrin type-A receptor 32.7.10.10.458
4hyi1AOSerine/threonine-protein kinase Chk12.7.11.10.458
4mv8ACPBiotin carboxylase6.3.4.140.458
1dm2HMDCyclin-dependent kinase 22.7.11.220.457
1q41IXMGlycogen synthase kinase-3 beta2.7.11.260.457
2dwpACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.457
2hy0306Serine/threonine-protein kinase Chk12.7.11.10.457
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.457
3n0tOPYDipeptidyl peptidase 23.4.14.20.457
3nynSGVG protein-coupled receptor kinase 62.7.11.160.457
3rk507ZCyclin-dependent kinase 22.7.11.220.457
2fzmFADBifunctional protein PutA1.5.5.20.456
3e2sFADBifunctional protein PutA1.5.5.20.456
4acg6LQGlycogen synthase kinase-3 beta2.7.11.260.456
4g6nEK0Mitogen-activated protein kinase 12.7.11.240.456
4h3qANPMitogen-activated protein kinase 12.7.11.240.456
4nm9FADBifunctional protein PutA/0.456
4oacADPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.456
1py5PY1TGF-beta receptor type-12.7.11.300.455
2ayp43ASerine/threonine-protein kinase Chk12.7.11.10.455
2vttLZDCyclin-dependent kinase 22.7.11.220.455
2ym7YM7Serine/threonine-protein kinase Chk12.7.11.10.455
3pdqKC6Lysine-specific demethylase 4A1.14.110.455
3t113T1Gag-Pol polyprotein3.4.23.160.455
4erwSTUCyclin-dependent kinase 22.7.11.220.455
4g170VNCasein kinase I isoform gamma-32.7.11.10.455
4m4922YL-lactate dehydrogenase A chain1.1.1.270.455
5dhhDGWNociceptin receptor/0.455
1ykr628Cyclin-dependent kinase 22.7.11.220.454
2c3kABOSerine/threonine-protein kinase Chk12.7.11.10.454
2cchATPCyclin-dependent kinase 22.7.11.220.454
2e9v85ASerine/threonine-protein kinase Chk12.7.11.10.454
2hxq373Serine/threonine-protein kinase Chk12.7.11.10.454
3iok1P6Tyrosine-protein kinase JAK2/0.454
3nuuJOZ3-phosphoinositide-dependent protein kinase 12.7.11.10.454
3s2pPMUCyclin-dependent kinase 22.7.11.220.454
4bgg844Activin receptor type-12.7.11.300.454
4fv1EK4Mitogen-activated protein kinase 12.7.11.240.454
4gh2HK0Serine/threonine-protein kinase Chk12.7.11.10.454
4kikKSAInhibitor of nuclear factor kappa-B kinase subunit beta2.7.11.100.454
1gih1PUCyclin-dependent kinase 22.7.11.220.453
1pyePM1Cyclin-dependent kinase 22.7.11.220.453
1r2jFADFkbI/0.453
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.453
2ydiYDISerine/threonine-protein kinase Chk12.7.11.10.453
3r1yX76Cyclin-dependent kinase 22.7.11.220.453
3r8zZ63Cyclin-dependent kinase 22.7.11.220.453
3rjc06ZCyclin-dependent kinase 22.7.11.220.453
4bdcODHSerine/threonine-protein kinase Chk22.7.11.10.453
4dgnLU2Casein kinase II subunit alpha2.7.11.10.453
4tv3ML9Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.453
2duv371Cyclin-dependent kinase 22.7.11.220.452
2vtqLZACyclin-dependent kinase 22.7.11.220.452
3cgcCOACoenzyme A disulfide reductase/0.452
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.452
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.452
1gii1PUCyclin-dependent kinase 22.7.11.220.451
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.451
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.451
3dogNNNCyclin-dependent kinase 22.7.11.220.451
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
3rwpABQ3-phosphoinositide-dependent protein kinase 12.7.11.10.451
4an4DUDPutative glycosyl transferase/0.451
4eoi1ROCyclin-dependent kinase 22.7.11.220.451
4i231C9Epidermal growth factor receptor2.7.10.10.451
4lyn1YGCyclin-dependent kinase 22.7.11.220.451
2itqITQEpidermal growth factor receptor2.7.10.10.450
2p4yC03Peroxisome proliferator-activated receptor gamma/0.450
3kgaLX9MAP kinase-activated protein kinase 22.7.11.10.450
3vf9477Tyrosine-protein kinase SYK2.7.10.20.450
4a84DXCMajor pollen allergen Bet v 1-A/0.450
4mv1ADPBiotin carboxylase6.3.4.140.450
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
2c6tDT5Cyclin-dependent kinase 22.7.11.220.449
2vd5BI8Myotonin-protein kinase2.7.11.10.449
2x1nX1NCyclin-dependent kinase 22.7.11.220.449
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
3hx4ANPCalmodulin-domain protein kinase 1/0.449
3rdqDTBStreptavidin/0.449
3ukuC69Actin-related protein 3/0.449
4a99FADTetX family tetracycline inactivation enzyme/0.449
4aacAAVMitogen-activated protein kinase 14/0.449
4c02TAKActivin receptor type-12.7.11.300.449
4fv9E71Mitogen-activated protein kinase 12.7.11.240.449
4jq8KJ8Epidermal growth factor receptor2.7.10.10.449
1y91CT9Cyclin-dependent kinase 22.7.11.220.448
2hk51BMTyrosine-protein kinase HCK2.7.10.20.448
2iw84SPCyclin-dependent kinase 22.7.11.220.448
3f7z34OGlycogen synthase kinase-3 beta2.7.11.260.448
3r1sX73Cyclin-dependent kinase 22.7.11.220.448
4bcqTJFCyclin-dependent kinase 22.7.11.220.448
1civNAPMalate dehydrogenase [NADP], chloroplastic1.1.1.820.447
2a0cCK9Cyclin-dependent kinase 22.7.11.220.447
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.447
2pe24643-phosphoinositide-dependent protein kinase 12.7.11.10.447
2r3lSCWCyclin-dependent kinase 22.7.11.220.447
2vr1ATFBiotin carboxylase6.3.4.140.447
2ycfYCFSerine/threonine-protein kinase Chk22.7.11.10.447
3hrcATP3-phosphoinositide-dependent protein kinase 12.7.11.10.447
3sw418KCyclin-dependent kinase 22.7.11.220.447
3tea4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.447
4bddZ0OSerine/threonine-protein kinase Chk22.7.11.10.447
4fko20KCyclin-dependent kinase 22.7.11.220.447
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.447
1fm4DXCMajor pollen allergen Bet v 1-L/0.446
1me6IVSPlasmepsin-23.4.23.390.446
1q3wATUGlycogen synthase kinase-3 beta2.7.11.260.446
1rw8580TGF-beta receptor type-12.7.11.300.446
2b9fADPMitogen-activated protein kinase FUS32.7.11.240.446
2iw94SPCyclin-dependent kinase 22.7.11.220.446
2q59240Peroxisome proliferator-activated receptor gamma/0.446
3qtrX36Cyclin-dependent kinase 22.7.11.220.446
3sheI85MAP kinase-activated protein kinase 32.7.11.10.446
4bis8HQLysine-specific demethylase 4A1.14.110.446
4eutBX7Serine/threonine-protein kinase TBK12.7.11.10.446
4hgl0YOCasein kinase I isoform gamma-32.7.11.10.446
4hyh1AMSerine/threonine-protein kinase Chk12.7.11.10.446
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.446
1j39UPGDNA beta-glucosyltransferase/0.445
1ke9LS5Cyclin-dependent kinase 22.7.11.220.445
1q5kTMUGlycogen synthase kinase-3 beta2.7.11.260.445
1u30GOXPancreatic alpha-amylase/0.445
1u33LM2Pancreatic alpha-amylase/0.445
2xbjXBJSerine/threonine-protein kinase Chk22.7.11.10.445
2ycsNXPSerine/threonine-protein kinase Chk22.7.11.10.445
3qcs3Q13-phosphoinositide-dependent protein kinase 12.7.11.10.445
4dgo0JWCasein kinase II subunit alpha2.7.11.10.445
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4ftq4HKSerine/threonine-protein kinase Chk12.7.11.10.445
4jq7KJQEpidermal growth factor receptor2.7.10.10.445
4l4dCAMCamphor 5-monooxygenase1.14.15.10.445
4yzcSTUSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.445
1aq1STUCyclin-dependent kinase 22.7.11.220.444
1gij2PUCyclin-dependent kinase 22.7.11.220.444
1pdhFASp-hydroxybenzoate hydroxylase/0.444
1tj2FADBifunctional protein PutA1.5.5.20.444
1urwI1PCyclin-dependent kinase 22.7.11.220.444
1vjy460TGF-beta receptor type-12.7.11.300.444
2bheBRYCyclin-dependent kinase 22.7.11.220.444
2c6o4SPCyclin-dependent kinase 22.7.11.220.444
2uzbC75Cyclin-dependent kinase 22.7.11.220.444
3lfnA27Cyclin-dependent kinase 22.7.11.220.444
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.444
3tnwF18Cyclin-dependent kinase 22.7.11.220.444
4bdiHAUSerine/threonine-protein kinase Chk22.7.11.10.444
1ckpPVBCyclin-dependent kinase 22.7.11.220.443
1h1r6CPCyclin-dependent kinase 22.7.11.220.443
1m2rMNYCasein kinase II subunit alpha2.7.11.10.443
1v0pPVBCell division control protein 2 homolog2.7.11.220.443
2cciATPCyclin-dependent kinase 22.7.11.220.443
2q55MU0Protease/0.443
3a62STURibosomal protein S6 kinase beta-12.7.11.10.443
3lpbNVBTyrosine-protein kinase JAK2/0.443
3rk909ZCyclin-dependent kinase 22.7.11.220.443
4a81DXCMajor pollen allergen Bet v 1-A/0.443
4acc7YGGlycogen synthase kinase-3 beta2.7.11.260.443
4aqc88ATyrosine-protein kinase JAK2/0.443
4bcnT9NCyclin-dependent kinase 22.7.11.220.443
4oh4ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.443
4r3aRBFBlue-light-activated histidine kinase 22.7.13.30.443
4u9aSTUInterleukin-1 receptor-associated kinase 42.7.11.10.443
5e8wSTUTGF-beta receptor type-12.7.11.300.443
1omoNADAlanine dehydrogenase/0.442
1ydrIQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2cdz23DSerine/threonine-protein kinase PAK 42.7.11.10.442
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
2csnCKICasein kinase I homolog 12.7.11.10.442
2v58LZJBiotin carboxylase6.3.4.140.442
2ym6YM6Serine/threonine-protein kinase Chk12.7.11.10.442
3qqgX06Cyclin-dependent kinase 22.7.11.220.442
3qu0X40Cyclin-dependent kinase 22.7.11.220.442
3rpv26ZCyclin-dependent kinase 22.7.11.220.442
3uvp048Mitogen-activated protein kinase 14/0.442
4ek610KCyclin-dependent kinase 22.7.11.220.442
4fks46KCyclin-dependent kinase 22.7.11.220.442
4gmy0X5Tyrosine-protein kinase JAK2/0.442
4hgs15GCasein kinase I isoform gamma-32.7.11.10.442
4q5jANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.442
1fvt106Cyclin-dependent kinase 22.7.11.220.441
2i1vADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.441
2q7vFADThioredoxin reductase/0.441
2yjxYJXHeat shock protein HSP 90-alpha/0.441
3ezrEZRCyclin-dependent kinase 22.7.11.220.441
3oom507Activin receptor type-12.7.11.300.441
3pvuQRWBeta-adrenergic receptor kinase 12.7.11.150.441
3zh8C58Protein kinase C iota type2.7.11.130.441
4bieIE6Mitogen-activated protein kinase kinase kinase 52.7.11.250.441
4fkw62KCyclin-dependent kinase 22.7.11.220.441
4ftkH9KSerine/threonine-protein kinase Chk12.7.11.10.441
4h4xFADBiphenyl dioxygenase ferredoxin reductase subunit/0.441
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.441
4ockANPN-acetylhexosamine 1-kinase2.7.1.1620.441
6cp4CAMCamphor 5-monooxygenase1.14.15.10.441
1m17AQ4Epidermal growth factor receptor2.7.10.10.440
1oirHDYCyclin-dependent kinase 22.7.11.220.440
1rx8NAPDihydrofolate reductase1.5.1.30.440
1xkkFMMEpidermal growth factor receptor2.7.10.10.440
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.440
2pvnP63Casein kinase II subunit alpha2.7.11.10.440
2uzeC95Cyclin-dependent kinase 22.7.11.220.440
2wouZZFTGF-beta receptor type-12.7.11.300.440
2ym44YMSerine/threonine-protein kinase Chk12.7.11.10.440
3iogSDFMetallo-beta-lactamase type 2/0.440
3lqfNADGalactitol dehydrogenase/0.440
3sw719KCyclin-dependent kinase 22.7.11.220.440
4a8v2ANMajor pollen allergen Bet v 1-J/0.440
4fki09KCyclin-dependent kinase 22.7.11.220.440
4gih0X5Non-receptor tyrosine-protein kinase TYK22.7.10.20.440
4jqeANPCasein kinase II subunit alpha2.7.11.10.440
4rrvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.440
5dr6SKEAurora kinase A2.7.11.10.440