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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
4h0tLARActin, alpha skeletal muscle

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4h0tLARActin, alpha skeletal muscle/1.000
4h0yLARActin, alpha skeletal muscle/0.810
4gy2LARActin, alpha skeletal muscle/0.731
4b1uLABActin, alpha skeletal muscle/0.675
3sjhLARActin, alpha skeletal muscle/0.641
1rdwLARActin, alpha skeletal muscle/0.640
3buzLARActin, alpha skeletal muscle/0.638
2q0uLABActin, alpha skeletal muscle/0.635
2v51LABActin, alpha skeletal muscle/0.634
2v52LABActin, alpha skeletal muscle/0.629
4b1vATPActin, alpha skeletal muscle/0.627
4b1vLABActin, alpha skeletal muscle/0.619
1ijjLARActin, alpha skeletal muscle/0.602
1sqkLARActin, alpha skeletal muscle/0.600
4h03LARActin, alpha skeletal muscle/0.600
1esvLARActin, alpha skeletal muscle/0.547
3chwATPMajor actin/0.547
4pl8ATPActin, alpha skeletal muscle/0.544
1rfqATPActin, alpha skeletal muscle/0.539
1rfqLARActin, alpha skeletal muscle/0.534
4g3pUD1Bifunctional protein GlmU/0.497
4bdgP3JSerine/threonine-protein kinase Chk22.7.11.10.495
2j2pSC2Ficolin-2/0.491
2vwpNDPGlucose 1-dehydrogenase/0.491
3rgaLSBEpoxide hydrolase LasB5.5.10.480
4tx9AMZPhosphoribosyl isomerase A/0.479
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.478
1r31MEV3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.475
4jhz1KVBeta-glucuronidase3.2.1.310.475
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.473
4y9qC2EUncharacterized protein/0.472
3t54ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.470
5auuLU2Death-associated protein kinase 12.7.11.10.470
2vwqNAPGlucose 1-dehydrogenase/0.469
3h03UBPGlutamate receptor 2/0.469
4n3e2ANPhenolic oxidative coupling protein/0.469
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.468
2e9p77ASerine/threonine-protein kinase Chk12.7.11.10.465
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.465
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
2ad5ADPCTP synthase/0.464
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.464
3zo4QWIcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.464
1hmp5GPHypoxanthine-guanine phosphoribosyltransferase2.4.2.80.463
1rejB1LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.463
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.463
4fyo0VFTyrosine-protein kinase SYK2.7.10.20.463
2j0sANPEukaryotic initiation factor 4A-III3.6.4.130.462
2uzlC94Cyclin-dependent kinase 22.7.11.220.462
1n07FMNRiboflavin kinase2.7.1.260.461
2qhm7CSSerine/threonine-protein kinase Chk12.7.11.10.460
3ugc046Tyrosine-protein kinase JAK2/0.460
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
1wvxBD4Death-associated protein kinase 12.7.11.10.459
1y56FMNUncharacterized protein/0.459
1y56FMN382aa long hypothetical sarcosine oxidase/0.459
2wouZZFTGF-beta receptor type-12.7.11.300.459
3pcrGTPADP-ribosylation factor 6/0.459
3u9n09HSerine/threonine-protein kinase Chk12.7.11.10.459
2vo0M03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
3coy53HPantothenate synthetase6.3.2.10.457
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.457
3c34KAIGlutamate receptor ionotropic, kainate 1/0.456
2vwhNAPGlucose 1-dehydrogenase/0.455
2c3lIDZSerine/threonine-protein kinase Chk12.7.11.10.454
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
4dpwAGSMevalonate diphosphate decarboxylase/0.454
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
2apcUDMAlpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.453
2oz6CMPCyclic AMP receptor-like protein/0.453
4bdiHAUSerine/threonine-protein kinase Chk22.7.11.10.453
4z54GDPNeuronal-specific septin-3/0.453
3cnpSP7Polyamine oxidase FMS1/0.452
4fic0ULProto-oncogene tyrosine-protein kinase Src2.7.10.20.452
1c0fATPMajor actin/0.451
3i7eDJRGag-Pol polyprotein/0.451
1omoNADAlanine dehydrogenase/0.450
1uu7BI23-phosphoinositide-dependent protein kinase 12.7.11.10.450
2cdz23DSerine/threonine-protein kinase PAK 42.7.11.10.450
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
4ehtADP2-hydroxyisocaproyl-CoA dehydratase activator/0.450
1w2xRCPAcetyl-CoA carboxylase/0.449
2cu0XMPInosine-5'-monophosphate dehydrogenase/0.449
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
1u28NAPNAD(P) transhydrogenase subunit beta1.6.1.20.448
1uadGNPRas-related protein Ral-A/0.448
2b0qADPAminoglycoside 3'-phosphotransferase2.7.1.950.448
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.448
3jxwLXGSerine/threonine-protein kinase pim-12.7.11.10.448
3qruX19Cyclin-dependent kinase 22.7.11.220.448
4iwyADPRibosomal protein S6--L-glutamate ligase/0.448
1atnATPActin, alpha skeletal muscle/0.447
2b5vNAPGlucose 1-dehydrogenase/0.447
2uw0GVKcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
3adcANPL-seryl-tRNA(Sec) kinase2.7.1.1640.447
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.447
4tvbNADHomospermidine synthase2.5.1.440.447
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.446
2qnqQN3Gag-Pol polyprotein3.4.23.160.446
3aglA03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3okxSAMS-adenosyl-L-methionine-binding protein RPA0152/0.446
4ftjH8KSerine/threonine-protein kinase Chk12.7.11.10.446
1j39UPGDNA beta-glucosyltransferase/0.445
2brhDFWSerine/threonine-protein kinase Chk12.7.11.10.445
3ggu017Gag-Pol polyprotein3.4.23.160.445
3t9aANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.445
5f0a1FBcGMP-dependent protein kinase, putative/0.445
3isjA8DPantothenate synthetase6.3.2.10.444
3nizADPCdc2-like CDK2/CDC28 like protein kinase/0.444
5d9j0N8Polymerase acidic protein/0.444
1i9c5ADGlutamate mutase epsilon subunit/0.443
1kzkJE2Gag-Pol polyprotein3.4.23.160.443
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.443
1qpePP2Tyrosine-protein kinase Lck2.7.10.20.443
1tqpATPRIO-type serine/threonine-protein kinase Rio22.7.11.10.443
1xh9R69cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
2yvfFADFerredoxin reductase/0.443
4enxZ20Serine/threonine-protein kinase pim-12.7.11.10.443
4g3sUD1Bifunctional protein GlmU/0.443
4l435FIRibosomal protein S6 kinase beta-12.7.11.10.443
4lj8ADPChaperone protein ClpB/0.443
4lrrCF9Thymidylate synthase/0.443
1yqy915Lethal factor3.4.24.830.442
2p55MRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.442
2y882ERPhosphoribosyl isomerase A5.3.1.160.442
3dpd41APhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
3gcvSS6Mitogen-activated protein kinase 14/0.442
3imeBZ2Pantothenate synthetase6.3.2.10.442
4yqfGDPSeptin-9/0.442
1me7RVPInosine-5'-monophosphate dehydrogenase/0.441
1svhI08cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.441
2vnwM01cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2vo3M04cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
4c2pX8ZAngiotensin-converting enzyme3.2.10.441
4k4p3TLGag-Pol polyprotein/0.441
1tj2FADBifunctional protein PutA1.5.5.20.440
2xizXIZSerine/threonine-protein kinase pim-12.7.11.10.440
3nwxKVSGag-Pol polyprotein3.4.23.160.440
3uq6ADNPutative adenosine kinase/0.440
3vjoANPEpidermal growth factor receptor2.7.10.10.440
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4feq0T8Tyrosine-protein kinase receptor TYRO32.7.10.10.440
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4xvuATPATPase GET3/0.440