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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
1t48BB3Tyrosine-protein phosphatase non-receptor type 13.1.3.48

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1t48BB3Tyrosine-protein phosphatase non-receptor type 13.1.3.481.000
4nbl2J6Caspase-63.4.22.590.485
1ozqPRFQueuine tRNA-ribosyltransferase2.4.2.290.484
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.482
2vt4P32Beta-1 adrenergic receptor/0.477
4fa30SLAldo-keto reductase family 1 member C3/0.475
4kbn25UDihydrofolate reductase1.5.1.30.475
3hv3R49Mitogen-activated protein kinase 14/0.474
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.474
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.473
3bbfGDPNucleoside diphosphate kinase B2.7.4.60.473
3lfeZ84Mitogen-activated protein kinase 14/0.473
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.473
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.472
2bjsACVIsopenicillin N synthase1.21.3.10.472
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.470
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.469
1cl2PPGCystathionine beta-lyase MetC4.4.1.80.468
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.468
4b4vL34Bifunctional protein FolD/0.467
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.466
1ygjRMCPyridoxal kinase2.7.1.350.466
2zhf49UProthrombin3.4.21.50.466
3p9tTCLRepressor/0.466
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.466
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.466
1y5xE89Queuine tRNA-ribosyltransferase2.4.2.290.465
2fmn4HF5,10-methylenetetrahydrofolate reductase1.5.1.200.465
2gsqGBIGlutathione S-transferase2.5.1.180.465
3arvSAUChitinase A/0.465
4iaq2GM5-hydroxytryptamine receptor 1B/0.465
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.464
1y6qTDI5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase3.2.2.90.464
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.463
2yatEEUEstrogen receptor/0.463
3nu03TUDihydrofolate reductase1.5.1.30.463
2fzjDH3Dihydrofolate reductase1.5.1.30.462
2y60M8FIsopenicillin N synthase1.21.3.10.462
4b4w9L9Bifunctional protein FolD/0.462
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.462
4pnmNU1Tankyrase-22.4.2.300.462
1oc1ASVIsopenicillin N synthase1.21.3.10.461
1qtiGNTAcetylcholinesterase3.1.1.70.460
2bu9HFVIsopenicillin N synthase1.21.3.10.460
2xvw9NRSerum albumin/0.460
1dghNDPCatalase1.11.1.60.459
2tplHPPTyrosine phenol-lyase4.1.99.20.459
4a6dSAMAcetylserotonin O-methyltransferase2.1.1.40.459
2yczI32Beta-1 adrenergic receptor/0.459
1blzACVIsopenicillin N synthase1.21.3.10.458
3u3o3QVSulfotransferase 1A12.8.2.10.458
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.458
4do30LAFatty-acid amide hydrolase 13.5.1.990.458
4iarERM5-hydroxytryptamine receptor 1B/0.458
2hxzH7JCathepsin S3.4.22.270.457
2rd2QSIGlutamine--tRNA ligase6.1.1.180.457
2x20PIDPeridinin-chlorophyll a-binding protein 1, chloroplastic/0.457
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.457
3gieACPSensor histidine kinase DesK2.7.13.30.457
3nwlNDPCatalase1.11.1.60.457
3qly55VUncharacterized protein/0.457
4dz5NAPAldo-keto reductase family 1 member C3/0.457
4mrxCZHObelin/0.457
1e62FADFerredoxin--NADP reductase1.18.1.20.456
1jxzBCA4-chlorobenzoyl coenzyme A dehalogenase3.8.1.70.456
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.456
2i16LDTAldose reductase1.1.1.210.456
2vbpVB1Isopenicillin N synthase1.21.3.10.456
4qij1HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.456
1bk0ACVIsopenicillin N synthase1.21.3.10.455
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
1kmvLIIDihydrofolate reductase1.5.1.30.455
3h4vDVPPteridine reductase 11.5.1.330.455
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.455
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
2re8GSUGlutamine--tRNA ligase6.1.1.180.454
2xtbKRMAdenosine kinase, putative/0.454
3gcq1BUMitogen-activated protein kinase 14/0.454
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
5kf2COAPredicted acetyltransferase/0.454
2bf7HBIPteridine reductase 11.5.1.330.453
2poqISDTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase1.3.1.200.453
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.453
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.453
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.453
4zasTYDCalS13/0.453
1e2lTMCThymidine kinase/0.452
1w19T4P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.452
3djfBC3Purine nucleoside phosphorylase/0.452
4ddrMMVDihydrofolate reductase1.5.1.30.452
4h7zGUNQueuine tRNA-ribosyltransferase2.4.2.290.452
1gj5130Prothrombin3.4.21.50.451
1h42FADFerredoxin--NADP reductase1.18.1.20.451
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.451
2iltNN1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3arpDEQChitinase A/0.451
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
3zkyWT4Isopenicillin N synthase1.21.3.10.451
4xzjNADPutative NAD(+)--arginine ADP-ribosyltransferase Vis2.4.2.310.451
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.450
1votHUPAcetylcholinesterase3.1.1.70.450
2qhxFE1Pteridine reductase 11.5.1.330.450
2qxwLDTAldose reductase1.1.1.210.450
2wjoQUDBeta-secretase 13.4.23.460.450
3nxyD2HDihydrofolate reductase1.5.1.30.450
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.450
4f1tH52Probable serine/threonine-protein kinase roco42.7.11.10.450
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.450
1d3dBZTProthrombin3.4.21.50.449
1s3yTQTDihydrofolate reductase1.5.1.30.449
3s41S41Glucokinase2.7.1.20.449
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.449
3zpqXF5Beta-1 adrenergic receptor/0.449
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.449
4c717RD3-oxoacyl-ACP synthase/0.449
4n3l2FNProthrombin3.4.21.50.449
1obnASVIsopenicillin N synthase1.21.3.10.448
1pd8CO4Dihydrofolate reductase1.5.1.30.448
1qv0CZHObelin/0.448
1s3uTQDDihydrofolate reductase1.5.1.30.448
2vcmM11Isopenicillin N synthase1.21.3.10.448
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.448
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.448
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.448
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.448
3qwc98PProthrombin3.4.21.50.448
3szfDCQSulfide-quinone reductase/0.448
3x0c5GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.448
4c6zTLE3-oxoacyl-ACP synthase/0.448
4dhyS41Glucokinase2.7.1.20.448
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
4kd79DRDihydrofolate reductase1.5.1.30.448
5ab7MLCNonspecific lipid-transfer protein, putative/0.448
5h8tRTLRetinol-binding protein 1/0.448
1zq5E04Aldo-keto reductase family 1 member C3/0.447
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
3aklADPSerine/threonine-protein kinase CtkA2.7.11.10.447
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4ea0651Dehydrosqualene synthase/0.447
1be4PCGNucleoside diphosphate kinase A 22.7.4.60.446
1oytFSNProthrombin3.4.21.50.446
2a9z26AAdenosine kinase2.7.1.200.446
2bnpMSTReaction center protein L chain/0.446
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.446
2uuk897Prothrombin3.4.21.50.446
3o9lLPNRenin3.4.23.150.446
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.446
4fhd0TTSpore photoproduct lyase/0.446
1dr4HBIDihydrofolate reductase1.5.1.30.445
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.445
1ohkCOPDihydrofolate reductase1.5.1.30.445
2qx7NAPEugenol synthase 11.1.1.3180.445
3k4551PDihydrofolate reductase1.5.1.30.445
3qiyQI1Botulinum neurotoxin type A3.4.24.690.445
4b1iA8PPoly(ADP-ribose) glycohydrolase3.2.1.1430.445
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.445
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.445
4mryCEIObelin/0.445
4muw2F4cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4u0oMTALipoyl synthase 2/0.445
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.444
1lnmDTXBilin-binding protein/0.444
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
1qiqACCIsopenicillin N synthase1.21.3.10.444
1yryMSGPurine nucleoside phosphorylase2.4.2.10.444
2io6330Wee1-like protein kinase2.7.10.20.444
2w6cBM4Acetylcholinesterase3.1.1.70.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.444
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.444
3ghh2NFCD38 molecule/0.444
3mauPLRPutative sphingosine-1-phosphate lyase/0.444
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.444
4jxxATPGlutamine--tRNA ligase6.1.1.180.444
4nbjD3YD-tyrosyl-tRNA(Tyr) deacylase/0.444
4oex5EOcGMP-specific 3',5'-cyclic phosphodiesterase/0.444
4phlPILPhosphodiesterase/0.444
4x24TDI5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/0.444
4yfy1YJVioF/0.444
4z87GDPInosine-5'-monophosphate dehydrogenase/0.444
1jf2CZHObelin/0.443
1sjwNGVNogalonic acid methyl ester cyclase/0.443
2jh0701Prothrombin3.4.21.50.443
2jj2ADPATP synthase subunit alpha, mitochondrial/0.443
2jj2ADPATP synthase subunit beta, mitochondrial3.6.3.140.443
2rqfJH3Hemolymph juvenile hormone binding protein/0.443
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.443
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3cqeP91Wee1-like protein kinase2.7.10.20.443
3gyf51PDihydrofolate reductase1.5.1.30.443
3iej599Cathepsin S3.4.22.270.443
3ptzUDXUDP-glucose 6-dehydrogenase1.1.1.220.443
3vf60H6Glucokinase2.7.1.20.443
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.443
4k6i9RARetinoic acid receptor RXR-alpha/0.443
4nbn2J7Caspase-63.4.22.590.443
3emlZMAAdenosine receptor A2a/0.443
1dlrMXADihydrofolate reductase1.5.1.30.442
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1hb1OCVIsopenicillin N synthase1.21.3.10.442
1w2cANPInositol-trisphosphate 3-kinase A2.7.1.1270.442
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2b04CHOPhospholipase A2, major isoenzyme3.1.1.40.442
2q6hCXXNa(+):neurotransmitter symporter (Snf family)/0.442
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3eon341Glutaryl-CoA dehydrogenase/0.442
3jq6DX1Pteridine reductase, putative/0.442
3lm4HPXCatechol 2,3-dioxygenase/0.442
3njoPYVAbscisic acid receptor PYR1/0.442
3nxrD2DDihydrofolate reductase1.5.1.30.442
4bjbP34Tankyrase-22.4.2.300.442
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.442
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.442
4k9yK9YFocal adhesion kinase 12.7.10.20.442
4nhyPD2Prolyl 3-hydroxylase OGFOD11.14.110.442
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.442
1dgfNDPCatalase1.11.1.60.441
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.441
1pd9CO4Dihydrofolate reductase1.5.1.30.441
1pwmFIDAldose reductase1.1.1.210.441
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2vz0D64Pteridine reductase/0.441
3d73NBBPheromone-binding protein ASP1/0.441
4bfuZVUPantothenate kinase2.7.1.330.441
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.441
4y6nUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.441
5d7pAR6NAD-dependent protein deacetylase sirtuin-23.5.10.441
5epvACPBlue-light-activated histidine kinase2.7.13.30.441
5stdUNNScytalone dehydratase4.2.1.940.441
1fcy564Retinoic acid receptor gamma/0.440
1kyyINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1odnAPVIsopenicillin N synthase1.21.3.10.440
1ry0PG2Aldo-keto reductase family 1 member C3/0.440
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
2bxqIMNSerum albumin/0.440
2iqdLPAAldose reductase1.1.1.210.440
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.440
2vqjTFGHistone deacetylase 43.5.1.980.440
2wo7ASVIsopenicillin N synthase1.21.3.10.440
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.440
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
3ug8IMNAldo-keto reductase family 1 member C3/0.440
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
4fsa0V3Queuine tRNA-ribosyltransferase2.4.2.290.440