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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2lbdREARetinoic acid receptor gamma

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2lbdREARetinoic acid receptor gamma/1.000
1fd0254Retinoic acid receptor gamma/0.695
1fcx184Retinoic acid receptor gamma/0.692
4dm6TTBRetinoic acid receptor beta/0.689
1fcy564Retinoic acid receptor gamma/0.668
4dm8REARetinoic acid receptor beta/0.667
1exa394Retinoic acid receptor gamma/0.637
1xdkREARetinoic acid receptor beta/0.602
3tdaPN0Cytochrome P450 2D6/0.543
1pkfEPDEpothilone C/D epoxidase1.140.514
1h36R88Squalene--hopene cyclase4.2.1.1290.511
3t8xT8XT-cell surface glycoprotein CD1b/0.509
4j6dTESCytochrome P450 monooxygenase/0.502
1iyzNDPProbable quinone oxidoreductase/0.501
3up3XCAaceDAF-12/0.495
1q5dEPBEpothilone C/D epoxidase1.140.494
1o6rR19Squalene--hopene cyclase4.2.1.1290.493
3qm4PN0Cytochrome P450 2D6/0.493
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.490
4iarERM5-hydroxytryptamine receptor 1B/0.490
4j6cSTRCytochrome P450 monooxygenase/0.490
5bp9SAHPutative methyltransferase protein/0.490
2culFADGidA-related protein/0.487
5dozNDPJamJ/0.487
4b8uIBK3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase4.2.1.590.486
2belCBOCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.483
2rjp886A disintegrin and metalloproteinase with thrombospondin motifs 43.4.24.820.483
3fmz2T1Retinol-binding protein 4/0.483
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.483
2ykiYKIHeat shock protein HSP 90-alpha/0.481
3q44D50M1 family aminopeptidase3.4.110.481
4ele31IDihydrofolate reductase/0.481
4jbtASDCytochrome P450 monooxygenase/0.481
2j9lATPH(+)/Cl(-) exchange transporter 5/0.478
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.478
1o6qR17Squalene--hopene cyclase4.2.1.1290.477
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.476
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.476
4j6bPLOCytochrome P450 monooxygenase/0.475
2q4wFADCytokinin dehydrogenase 71.5.99.120.474
4elb34RDihydrofolate reductase/0.473
3dl9V2HVitamin D 25-hydroxylase/0.472
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.472
2ykjYKJHeat shock protein HSP 90-alpha/0.471
3a1l2CCCytochrome P450/0.471
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.471
1h35R01Squalene--hopene cyclase4.2.1.1290.470
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.470
2b00GCHPhospholipase A2, major isoenzyme3.1.1.40.470
1n4hREANuclear receptor ROR-beta/0.469
2bktRPFRenin3.4.23.150.469
4iaq2GM5-hydroxytryptamine receptor 1B/0.469
1kzjCB3Thymidylate synthase/0.468
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.468
3jynNDPQuinone oxidoreductase/0.468
3up0D7SaceDAF-12/0.468
4dhyS41Glucokinase2.7.1.20.467
2fs4PZ1Renin3.4.23.150.466
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.466
3abaFLICytochrome P450/0.466
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.466
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.465
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.465
3reyXACAdenosine receptor A2a/0.465
1felFENRetinol-binding protein 4/0.464
2g274LGRenin3.4.23.150.464
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.464
2gvcFADThiol-specific monooxygenase1.14.130.463
2zb8IMNProstaglandin reductase 21.3.1.480.463
5uviZMAAdenosine receptor A2a/0.463
4irnFADAnaB/0.461
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
4awo99BHeat shock protein HSP 90-alpha/0.460
5dp2NAPCurF/0.460
5jtbZMAAdenosine receptor A2a/0.460
1yc2NADNAD-dependent protein deacylase 2/0.459
2dvlFADAcyl-CoA dehydrogenase/0.459
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.459
3fnfJPMEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.459
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.459
2dqsTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.458
3bhrTHGThymidylate synthase/0.458
3p6nDSOCamphor 5-monooxygenase1.14.15.10.458
3p6oETGCamphor 5-monooxygenase1.14.15.10.458
4iwv1J9Glucokinase2.7.1.20.458
4mfb29TGag-Pol polyprotein2.7.7.490.458
3p6mDSOCamphor 5-monooxygenase1.14.15.10.457
3p9tTCLRepressor/0.457
4b0j3MQ3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase4.2.1.590.457
5ab6CAANonspecific lipid-transfer protein, putative/0.457
5ab7MLCNonspecific lipid-transfer protein, putative/0.457
2z2w770Wee1-like protein kinase2.7.10.20.456
3hxfBD9Geranylgeranyl transferase type-2 subunit beta2.5.1.600.456
3zkyWT4Isopenicillin N synthase1.21.3.10.456
4fc00T2Serine/threonine-protein kinase B-raf2.7.11.10.456
2e48FADD-amino-acid oxidase1.4.3.30.455
2lfoGCHFatty acid-binding protein, liver/0.455
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
3uzcT4EAdenosine receptor A2a/0.455
1n4sCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.454
1qjfACSIsopenicillin N synthase1.21.3.10.454
1re9DSOCamphor 5-monooxygenase1.14.15.10.454
1xuoLA1Integrin alpha-L/0.454
2pswCOAN-alpha-acetyltransferase 50/0.454
3s41S41Glucokinase2.7.1.20.454
2q9fC3SCholesterol 24-hydroxylase/0.453
3ctj320Hepatocyte growth factor receptor2.7.10.10.453
3wixLC3Induced myeloid leukemia cell differentiation protein Mcl-1/0.453
1diuBDMDihydrofolate reductase1.5.1.30.452
2d29FADAcyl-CoA dehydrogenase/0.452
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.452
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
2rgjFADFlavin-containing monooxygenase/0.452
2vqoTFGHistone deacetylase 43.5.1.980.452
3c96FADFlavin-containing monooxygenase/0.452
3iw8HIZMitogen-activated protein kinase 14/0.452
3ix9MTXDihydrofolate reductase1.5.1.30.452
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
4jqh1MFAlr2278 protein/0.452
1kt3RTLRetinol-binding protein 4/0.451
1nq7ARLNuclear receptor ROR-beta/0.451
1ohkCOPDihydrofolate reductase1.5.1.30.451
2v0mKLNCytochrome P450 3A4/0.451
3kpkFADSulfide-quinone reductase/0.451
3qlhT27Gag-Pol polyprotein2.7.7.490.451
4gmgNAPYersiniabactin biosynthetic protein YbtU/0.451
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.450
2in6839Wee1-like protein kinase2.7.10.20.450
2jn3JN3Fatty acid-binding protein, liver/0.450
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.450
2zd1T27Gag-Pol polyprotein2.7.7.490.450
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.450
5k2bZMAAdenosine receptor A2a/0.450
3uzaT4GAdenosine receptor A2a/0.450
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1s7gNADNAD-dependent protein deacylase 2/0.449
1w22NHBHistone deacetylase 83.5.1.980.449
2aibERGBeta-elicitin cinnamomin/0.449
3g6zA7TRenin3.4.23.150.449
3vf60H6Glucokinase2.7.1.20.449
4elf35IDihydrofolate reductase/0.449
5k2cZMAAdenosine receptor A2a/0.449
1aqbRTLRetinol-binding protein 4/0.448
2dhfDZFDihydrofolate reductase1.5.1.30.448
2hq9FADMll6688 protein/0.448
3w8wFADPutative FAD-dependent oxygenase EncM/0.448
3zeiAWHO-acetylserine sulfhydrylase/0.448
1an5CB3Thymidylate synthase/0.447
1disBDMDihydrofolate reductase1.5.1.30.447
1oc1ASVIsopenicillin N synthase1.21.3.10.447
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
2y6fM9FIsopenicillin N synthase1.21.3.10.447
3cxhSMACytochrome b/0.447
3l6jZ90Alr2278 protein/0.447
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.447
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.447
3slkNDPPolyketide synthase extender module 2/0.447
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.447
5g53NECAdenosine receptor A2a/0.447
3rfmCFFAdenosine receptor A2a/0.447
2fhjMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.446
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.446
2yjxYJXHeat shock protein HSP 90-alpha/0.446
3r7kFDAProbable acyl CoA dehydrogenase/0.446
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
4c1mNIHMyeloperoxidase1.11.2.20.446
4eevL1XHepatocyte growth factor receptor2.7.10.10.446
4g1nNZTPyruvate kinase PKM2.7.1.400.446
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.446
4isk1JYThymidylate synthase/0.446
1drfFOLDihydrofolate reductase1.5.1.30.445
1s64778Geranylgeranyl transferase type-1 subunit beta2.5.1.590.445
2a4nCOAAac(6')-Ii protein/0.445
2aclL05Oxysterols receptor LXR-alpha/0.445
2b04CHOPhospholipase A2, major isoenzyme3.1.1.40.445
3l71AZOCytochrome b/0.445
4x28FDAAcyl-CoA dehydrogenase FadE26/0.445
4x28FDAAcyl-CoA dehydrogenase FadE27/0.445
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1hb1OCVIsopenicillin N synthase1.21.3.10.444
1pd9CO4Dihydrofolate reductase1.5.1.30.444
1rf9DBRCamphor 5-monooxygenase1.14.15.10.444
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2w98P1ZProstaglandin reductase 21.3.1.480.444
3oadLPORenin3.4.23.150.444
3tm5SFGUncharacterized protein/0.444
4a6eASEAcetylserotonin O-methyltransferase2.1.1.40.444
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.444
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.444
4r20AERCytochrome P450 family 17 polypeptide 2/0.444
4ybnFADFlavin-nucleotide-binding protein/0.444
1crbRTLRetinol-binding protein 1/0.443
2w4qCBWProstaglandin reductase 21.3.1.480.443
3cth319Hepatocyte growth factor receptor2.7.10.10.443
3ds6A17Mitogen-activated protein kinase 14/0.443
3gkjHC3Niemann-Pick C1 protein/0.443
3irxUDRGag-Pol polyprotein2.7.7.490.443
3t2kFADSulfide-quinone reductase/0.443
4cavMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.443
4elb34SDihydrofolate reductase/0.443
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
4ksp1SUSerine/threonine-protein kinase B-raf2.7.11.10.443
4qe6JN3Bile acid receptor/0.443
4ug2NGIAdenosine receptor A2a/0.443
1bk0ACVIsopenicillin N synthase1.21.3.10.442
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.442
1zhzERGOxysterol-binding protein homolog 4/0.442
2ob0ACON-alpha-acetyltransferase 50/0.442
2yiuSMACytochrome b/0.442
2ykeYKEHeat shock protein HSP 90-alpha/0.442
3ghvGHCDihydrofolate reductase1.5.1.30.442
3h6k33TCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3p6pA6BCamphor 5-monooxygenase1.14.15.10.442
3t14FADSulfide-quinone reductase/0.442
3vg9ZMAAdenosine receptor A2a/0.442
4aseAV9Vascular endothelial growth factor receptor 22.7.10.10.442
4at0FADPossible succinate dehydrogenase/0.442
4iah1DXAlr2278 protein/0.442
4k4eK4ETankyrase-12.4.2.300.442
4n3r2GUTankyrase-12.4.2.300.442
1e1kFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.441
1jomFFODihydrofolate reductase1.5.1.30.441
1m2hAPRNAD-dependent protein deacylase 1/0.441
1ppjANYCytochrome b/0.441
2ewpTXFEstrogen-related receptor gamma/0.441
2q3eUPGUDP-glucose 6-dehydrogenase1.1.1.220.441
3tvuB37Acetyl-CoA carboxylase/0.441
3vt65YIVitamin D3 receptor/0.441
4bfpSWYTankyrase-22.4.2.300.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
4o7uTHFThymidylate synthase/0.441
1b48HAGGlutathione S-transferase A42.5.1.180.440
1fwmCB3Thymidylate synthase/0.440
1hb3SCVIsopenicillin N synthase1.21.3.10.440
1jraFADFAD-linked sulfhydryl oxidase ERV21.8.3.20.440
1pz1NAPGeneral stress protein 69/0.440
2fonFADAcyl-coenzyme A oxidase/0.440
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
2z78H86Geranylgeranyl pyrophosphate synthase/0.440
3ol5SAWCamphor 5-monooxygenase1.14.15.10.440
3p99LNPLanosterol 14-alpha-demethylase/0.440
3sgtP09Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)/0.440
3t2zFADSulfide-quinone reductase/0.440
3u8hBHPPhospholipase A2, membrane associated/0.440
4fizCUE17beta-hydroxysteroid dehydrogenase/0.440
4hw219HInduced myeloid leukemia cell differentiation protein Mcl-1/0.440