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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
3ukrCKHActin-related protein 3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3ukrCKHActin-related protein 3/1.000
3ukrCKHActin-related protein 2/1.000
3dxkN23Actin-related protein 3/0.645
3dxkN23Actin-related protein 2/0.645
4pd6URINucleoside permease/0.507
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.493
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.482
2j5xGSPADP-ribosylation factor 6/0.481
2zlaVDBVitamin D3 receptor/0.480
1j39UPGDNA beta-glucosyltransferase/0.476
4ia1BIVVitamin D3 receptor A/0.472
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.471
2j5sKTAAlr4455 protein/0.470
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.470
4g1y0VOVitamin D3 receptor A/0.469
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.468
1lhvNOGSex hormone-binding globulin/0.468
4ia3BIVVitamin D3 receptor A/0.468
3n0tOPYDipeptidyl peptidase 23.4.14.20.467
4ez8DHFThymidylate synthase2.1.1.450.466
1ie8KH1Vitamin D3 receptor/0.465
4ia2BIVVitamin D3 receptor A/0.465
4rupH97Vitamin D3 receptor A/0.465
5fm7ADPRuvB-like helicase/0.465
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.464
3clbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.464
3p7cP7CMitogen-activated protein kinase 14/0.464
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.464
4iwyADPRibosomal protein S6--L-glutamate ligase/0.464
1nooCAHCamphor 5-monooxygenase1.14.15.10.463
4l425FIRibosomal protein S6 kinase beta-12.7.11.10.463
3a60STURibosomal protein S6 kinase beta-12.7.11.10.462
3rmf20ZCyclin-dependent kinase 22.7.11.220.462
1jpaANPEphrin type-B receptor 22.7.10.10.461
2hamC33Vitamin D3 receptor/0.461
2harOCCVitamin D3 receptor/0.461
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.461
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.461
4bdiHAUSerine/threonine-protein kinase Chk22.7.11.10.461
4l3l5FIRibosomal protein S6 kinase beta-12.7.11.10.461
4rujVDXVitamin D3 receptor A/0.461
1txiTX5Vitamin D3 receptor/0.460
2c0tL3GTyrosine-protein kinase HCK2.7.10.20.460
2jih097A disintegrin and metalloproteinase with thrombospondin motifs 13.4.240.460
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3uxyNADShort-chain dehydrogenase/reductase SDR/0.460
1db1VDXVitamin D3 receptor/0.459
1hpzAAPGag-Pol polyprotein2.7.7.490.459
3deiRXBCaspase-33.4.22.560.459
3sfuRBVPolyprotein/0.459
4ftiH7KSerine/threonine-protein kinase Chk12.7.11.10.459
4g090VDHistidinol dehydrogenase/0.459
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.459
1kt6RTLRetinol-binding protein 4/0.458
4fdnFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.458
5a3bAPRSIR2 family protein/0.458
2o4jVD4Vitamin D3 receptor/0.457
2qhn582Serine/threonine-protein kinase Chk12.7.11.10.457
2wipP49Cyclin-dependent kinase 22.7.11.220.457
3ocpCMPcGMP-dependent protein kinase 12.7.11.120.457
3sw719KCyclin-dependent kinase 22.7.11.220.457
3w0aDS5Vitamin D3 receptor/0.457
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
1ie9VDXVitamin D3 receptor/0.456
1nzdUPGDNA beta-glucosyltransferase/0.456
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.456
3vrwYS5Vitamin D3 receptor/0.456
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.456
1lriCLRBeta-elicitin cryptogein/0.455
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.455
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
2hcdBIVVitamin D3 receptor A/0.455
2np7NEAModification methylase TaqI2.1.1.720.455
2o7pNAPRiboflavin biosynthesis protein RibD/0.455
3vt3VDXVitamin D3 receptor/0.455
3zkyWT4Isopenicillin N synthase1.21.3.10.455
4g1z0VPVitamin D3 receptor A/0.455
5i39FADL-amino acid deaminase/0.455
1qoqIGPTryptophan synthase alpha chain/0.454
1sqvUHDCytochrome b/0.454
1w1rZEACytokinin dehydrogenase 11.5.99.120.454
2hc4VDXVitamin D3 receptor A/0.454
2vo3M04cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
3vtcTK3Vitamin D3 receptor/0.454
3w5q3KLVitamin D3 receptor/0.454
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
4fuxE75Mitogen-activated protein kinase 12.7.11.240.454
4g20484Vitamin D3 receptor A/0.454
4q0a4OAVitamin D3 receptor A/0.454
1iyzNDPProbable quinone oxidoreductase/0.453
1n4hREANuclear receptor ROR-beta/0.453
2hasC3OVitamin D3 receptor/0.453
2hb8MVDVitamin D3 receptor/0.453
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.453
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.453
3p7bP7BMitogen-activated protein kinase 14/0.453
3vruYS3Vitamin D3 receptor/0.453
4bdgP3JSerine/threonine-protein kinase Chk22.7.11.10.453
4g1d0VKVitamin D3 receptor A/0.453
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.452
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.452
2q9fC3SCholesterol 24-hydroxylase/0.452
2zgzGNPPlasmid segregation protein ParM/0.452
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3hk1B64Fatty acid-binding protein, adipocyte/0.452
3iqeH4MF420-dependent methylenetetrahydromethanopterin dehydrogenase1.5.98.10.452
3iqeF42F420-dependent methylenetetrahydromethanopterin dehydrogenase1.5.98.10.452
4if5ACOAlpha-tubulin N-acetyltransferase 1/0.452
1rekB8LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.451
4bdfH3RSerine/threonine-protein kinase Chk22.7.11.10.451
5a3cNADSIR2 family protein/0.451
4fhi0S4Vitamin D3 receptor A/0.450
4g2h0VQVitamin D3 receptor A/0.450
4qysPLRTryptophan synthase beta chain 24.2.1.200.450
2vtjLZ4Cyclin-dependent kinase 22.7.11.220.449
3d5qT30Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3mvhWFERAC-alpha serine/threonine-protein kinase2.7.11.10.449
3ral04ZCyclin-dependent kinase 22.7.11.220.449
3w0c6DSVitamin D3 receptor/0.449
3w0jT08Vitamin D3 receptor/0.449
4fic0ULProto-oncogene tyrosine-protein kinase Src2.7.10.20.449
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.449
4olfHFGProline--tRNA ligase6.1.1.150.449
4y93746Tyrosine-protein kinase/0.449
1h73ANPHomoserine kinase2.7.1.390.448
1kt3RTLRetinol-binding protein 4/0.448
2jedLG8Protein kinase C theta type2.7.11.130.448
3c3dFO12-phospho-L-lactate transferase/0.448
3d7tSTUTyrosine-protein kinase CSK/0.448
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3vt45YIVitamin D3 receptor/0.448
4eilUMPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.448
4g170VNCasein kinase I isoform gamma-32.7.11.10.448
4lgh0JNProto-oncogene tyrosine-protein kinase Src2.7.10.20.448
4ea30NNNociceptin receptor/0.448
1rkhVD2Vitamin D3 receptor/0.447
1t0iFMNNAD(P)H-dependent FMN reductase LOT6/0.447
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
3gkjHC3Niemann-Pick C1 protein/0.447
3vt5YI2Vitamin D3 receptor/0.447
3vt65YIVitamin D3 receptor/0.447
4dc0NDPPutative ketoacyl reductase1.3.10.447
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.447
4n3b12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.447
4ocvANPAminoglycoside phosphotransferase/0.447
5k2aZMAAdenosine receptor A2a/0.447
1ay0TPPTransketolase 12.2.1.10.446
1hvyD16Thymidylate synthase2.1.1.450.446
1qorNDPQuinone oxidoreductase 1/0.446
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.446
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.446
2hb7O1CVitamin D3 receptor/0.446
2ou2ACOHistone acetyltransferase KAT5/0.446
2x9dITCTetracycline repressor protein class D/0.446
2ykjYKJHeat shock protein HSP 90-alpha/0.446
3dndLL2cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3kpzZNEVitamin D3 receptor/0.446
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
3py0SU9Cyclin-dependent kinase 22.7.11.220.446
4fhh0U3Vitamin D3 receptor A/0.446
4iteTEYVitamin D3 receptor/0.446
5cdtPFBAlcohol dehydrogenase E chain1.1.1.10.446
1u4dDBQActivated CDC42 kinase 1/0.445
1w1sEMUCytokinin dehydrogenase 11.5.99.120.445
2pwuGUNQueuine tRNA-ribosyltransferase2.4.2.290.445
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3nuuJOZ3-phosphoinositide-dependent protein kinase 12.7.11.10.445
3rwpABQ3-phosphoinositide-dependent protein kinase 12.7.11.10.445
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.445
4i8vBHFCytochrome P450 1A11.14.14.10.445
4l8u9AZSerum albumin/0.445
4yryNADGlutamate synthase, beta subunit/0.445
2iw84SPCyclin-dependent kinase 22.7.11.220.444
2izrBRKCasein kinase I isoform gamma-32.7.11.10.444
2p15EZTEstrogen receptor/0.444
3tkuM77Serine/threonine-protein kinase MRCK beta2.7.11.10.444
3vydVYDRenin3.4.23.150.444
3vzcUULSphingosine kinase 12.7.1.910.444
4bdbODOSerine/threonine-protein kinase Chk22.7.11.10.444
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4iakADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
1kv1BMUMitogen-activated protein kinase 14/0.443
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.443
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.443
1ml6GBXGlutathione S-transferase A22.5.1.180.443
1uyfPU1Heat shock protein HSP 90-alpha/0.443
2o4rVD5Vitamin D3 receptor/0.443
2zl9VDAVitamin D3 receptor/0.443
3lm9ADPPutative fructokinase2.7.1.40.443
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.443
4gt3ATPMitogen-activated protein kinase 12.7.11.240.443
4itfTFYVitamin D3 receptor/0.443
4rrqA3SThreonine--tRNA ligase6.1.1.30.443
3pwhZMAAdenosine receptor A2a/0.443
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.442
1f5fDHTSex hormone-binding globulin/0.442
1l0lFMXCytochrome b/0.442
2an9GDPGuanylate kinase2.7.4.80.442
2nuaCOASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.442
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.442
2vbpVB1Isopenicillin N synthase1.21.3.10.442
2vttLZDCyclin-dependent kinase 22.7.11.220.442
3c3xNAPEugenol synthase 11.1.1.3180.442
3sgx0FWDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.442
4g210VPVitamin D3 receptor A/0.442
1fmjRTLRetinol dehydratase/0.441
1kzjCB3Thymidylate synthase/0.441
1ot7CHCBile acid receptor/0.441
1phhFADp-hydroxybenzoate hydroxylase/0.441
2hbhXE4Vitamin D3 receptor A/0.441
2hveADPNucleoside diphosphate kinase A2.7.4.60.441
2rhrEMOPutative ketoacyl reductase1.3.10.441
3ujlA8SAbscisic acid receptor PYL2/0.441
3zk5Z18Cytochrome P450 monooxygenase PikC/0.441
4bddZ0OSerine/threonine-protein kinase Chk22.7.11.10.441
4dbzNDPPutative ketoacyl reductase1.3.10.441
4eh9IRGMitogen-activated protein kinase 14/0.441
4eutBX7Serine/threonine-protein kinase TBK12.7.11.10.441
4fc00T2Serine/threonine-protein kinase B-raf2.7.11.10.441
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.440
1d7yFADFerredoxin reductase/0.440
1fm4DXCMajor pollen allergen Bet v 1-L/0.440
1fwmCB3Thymidylate synthase/0.440
1me7MOAInosine-5'-monophosphate dehydrogenase/0.440
2nadNADFormate dehydrogenase/0.440
2p9eNAID-3-phosphoglycerate dehydrogenase1.1.1.950.440
2pogWSTEstrogen receptor/0.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
2zb8IMNProstaglandin reductase 21.3.1.480.440
3gc9B45Mitogen-activated protein kinase 112.7.11.240.440
3h1jSMACytochrome b/0.440
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.440
3qtrX36Cyclin-dependent kinase 22.7.11.220.440
3qtuX44Cyclin-dependent kinase 22.7.11.220.440
3vryB43Tyrosine-protein kinase HCK2.7.10.20.440
3w0iO11Vitamin D3 receptor/0.440
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.440
3w5rLOAVitamin D3 receptor/0.440
4aicNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
4hw764MMacrophage colony-stimulating factor 1 receptor2.7.10.10.440
4l17DNQGlutamate receptor 2/0.440
4ly91YYGlucokinase regulatory protein/0.440
4mxyDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.440
4mxzDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.440
4nb6444Nuclear receptor ROR-gamma/0.440
4pnmNU1Tankyrase-22.4.2.300.440