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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
3m8cEQUSteroid Delta-isomerase5.3.3.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3m8cEQUSteroid Delta-isomerase5.3.3.11.000
2jb4A14Isopenicillin N synthase1.21.3.10.505
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.504
2vbdV10Isopenicillin N synthase1.21.3.10.500
2po7CHDFerrochelatase, mitochondrial4.99.1.10.498
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.493
3zoiM2WIsopenicillin N synthase1.21.3.10.489
3nhxASDSteroid Delta-isomerase5.3.3.10.488
1w7h3IPMitogen-activated protein kinase 14/0.483
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.483
3w33W19Epidermal growth factor receptor2.7.10.10.480
4q0kGA3Phytohormone-binding protein/0.480
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.479
1e3vDXCSteroid Delta-isomerase5.3.3.10.478
3d7zGK5Mitogen-activated protein kinase 14/0.478
1osvCHCBile acid receptor/0.477
3uayADNPurine nucleoside phosphorylase DeoD-type/0.477
4bfvZVVPantothenate kinase2.7.1.330.477
1zg32HIIsoflavone 4'-O-methyltransferase/0.476
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.475
1a8t061Metallo-beta-lactamase type 2/0.474
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.474
2i0ePDSProtein kinase C beta type2.7.11.130.474
3e5aVX6Aurora kinase A2.7.11.10.474
3poz03PEpidermal growth factor receptor2.7.10.10.474
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.473
1ndzFR5Adenosine deaminase3.5.4.40.473
4zowCLMMultidrug transporter MdfA/0.473
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
1kyzFERCaffeic acid 3-O-methyltransferase2.1.1.680.471
1jjeBYSBeta-lactamase/0.470
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.470
3zkyWT4Isopenicillin N synthase1.21.3.10.470
3vrzVRZTyrosine-protein kinase HCK2.7.10.20.469
4oztP1AEcdysone receptor, putative/0.469
1jtuLYBThymidylate synthase/0.468
1pr5TBNPurine nucleoside phosphorylase DeoD-type/0.468
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.468
4c1fX8ZMetallo-beta-lactamase type 2/0.468
1hb1OCVIsopenicillin N synthase1.21.3.10.467
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
4g310WHEukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.467
4ixc1JDGlucokinase2.7.1.20.467
1h36R88Squalene--hopene cyclase4.2.1.1290.466
1ot7IU5Bile acid receptor/0.466
3h3r14HCollagen type IV alpha-3-binding protein/0.466
1fm4DXCMajor pollen allergen Bet v 1-L/0.464
1ot7CHCBile acid receptor/0.464
2c0oL2GTyrosine-protein kinase HCK2.7.10.20.464
2a1uFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.463
3e92G6AMitogen-activated protein kinase 14/0.463
4jv41ORcAMP-dependent protein kinase type I-alpha regulatory subunit/0.463
2rbeZMGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.462
4a83DXCMajor pollen allergen Bet v 1-A/0.462
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.462
1w7kADPDihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.461
2flhZEACytokinin-specific binding protein/0.461
3arvSAUChitinase A/0.461
3c3xNAPEugenol synthase 11.1.1.3180.461
3da24MDCarbonic anhydrase 134.2.1.10.461
3dh7FMNIsopentenyl-diphosphate delta-isomerase/0.461
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.460
1uzwCDHIsopenicillin N synthase1.21.3.10.460
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.460
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.460
4qe6JN3Bile acid receptor/0.460
1qxlFR8Adenosine deaminase3.5.4.40.459
2e8sSAHDiphthine synthase/0.459
2qu6857Vascular endothelial growth factor receptor 22.7.10.10.459
2z3uCRRCytochrome P450/0.459
1o1vTCHGastrotropin/0.458
3ds6A17Mitogen-activated protein kinase 14/0.458
3l0lHC3Nuclear receptor ROR-gamma/0.458
3vf60H6Glucokinase2.7.1.20.458
4h2nFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.458
4k4fK4FTankyrase-12.4.2.300.458
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.458
5c1mCLRMu-type opioid receptor/0.458
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.457
1pz1NAPGeneral stress protein 69/0.457
2ol4JPNEnoyl-ACP reductase/0.457
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
3up0D7SaceDAF-12/0.457
4kwi1TJReductase homolog/0.457
4mv8ACPBiotin carboxylase6.3.4.140.457
1iepSTITyrosine-protein kinase ABL12.7.10.20.456
2c0tL3GTyrosine-protein kinase HCK2.7.10.20.456
2zb1GK4Mitogen-activated protein kinase 14/0.456
3tubFPUTyrosine-protein kinase SYK2.7.10.20.456
3w0aDS5Vitamin D3 receptor/0.456
3zbnCOA3-ketoacyl-CoA thiolase-like protein/0.456
4cjqVXOIntegrase/0.456
1jjtBDSBeta-lactamase/0.455
1ve3SAMUncharacterized protein/0.455
2c0iL1GTyrosine-protein kinase HCK2.7.10.20.455
2j83BATUlilysin3.4.240.455
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.455
5c93ACPTwo-component system histidine protein kinase/0.455
5hi2BAXSerine/threonine-protein kinase B-raf2.7.11.10.455
1oh0EQUSteroid Delta-isomerase5.3.3.10.454
1pr6XYAPurine nucleoside phosphorylase DeoD-type/0.454
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.454
3udk095Beta-secretase 13.4.23.460.454
3wixLC3Induced myeloid leukemia cell differentiation protein Mcl-1/0.454
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.454
4j6cSTRCytochrome P450 monooxygenase/0.454
1kqgMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.453
1powFADPyruvate oxidase1.2.3.30.453
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.453
3f883HTGlycogen synthase kinase-3 beta2.7.11.260.453
3hv3R49Mitogen-activated protein kinase 14/0.453
3w5tLHPVitamin D3 receptor/0.453
4jlk1NODeoxycytidine kinase2.7.1.740.453
1cbsREACellular retinoic acid-binding protein 2/0.452
1hpxKNIGag-Pol polyprotein/0.452
1r8qAFBCytohesin-2/0.452
1r8qAFBADP-ribosylation factor 1/0.452
2e16SAHDiphthine synthase/0.452
2f4jVX6Tyrosine-protein kinase ABL12.7.10.20.452
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.452
2znq401Peroxisome proliferator-activated receptor delta/0.452
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3fzt4JZProtein-tyrosine kinase 2-beta2.7.10.20.452
3i0pNADMalate dehydrogenase, putative/0.452
3owuEQUSteroid Delta-isomerase5.3.3.10.452
3p9tTCLRepressor/0.452
4hnc0UTMandelate racemase/0.452
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.452
4rh10TTSpore photoproduct lyase/0.452
1hb3SCVIsopenicillin N synthase1.21.3.10.451
1kqoDNDNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.451
1upw444Oxysterols receptor LXR-beta/0.451
3itzP66Mitogen-activated protein kinase 14/0.451
4dhyS41Glucokinase2.7.1.20.451
4e2xTYDMethyltransferase/0.451
4h4qFADBiphenyl dioxygenase ferredoxin reductase subunit/0.451
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.451
4qi5FADCellobiose dehydrogenase/0.451
1ci7CB3Thymidylate synthase2.1.1.450.450
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.450
1rsgFADPolyamine oxidase FMS1/0.450
1tl7FOKAdenylate cyclase type 2/0.450
1tl7FOKAdenylate cyclase type 5/0.450
2dxwSAHDiphthine synthase/0.450
2om9AJAPeroxisome proliferator-activated receptor gamma/0.450
2zfnACOHistone acetyltransferase RTT1092.3.1.480.450
3bhrTHGThymidylate synthase/0.450
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.450
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.450
3w32W32Epidermal growth factor receptor2.7.10.10.450
4a81DXCMajor pollen allergen Bet v 1-A/0.450
4fhf0TTSpore photoproduct lyase/0.450
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.450
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
4xybNDPFormate dehydrogenase/0.450
4zp0DXCMultidrug transporter MdfA/0.450
1obnASVIsopenicillin N synthase1.21.3.10.449
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.449
2a8xFADDihydrolipoyl dehydrogenase1.8.1.40.449
2eerNADNAD-dependent alcohol dehydrogenase1.1.1.10.449
3hv5R24Mitogen-activated protein kinase 14/0.449
3qlrNDPDihydrofolate reductase1.5.1.30.449
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.449
4psbGA3Cytokinin-specific binding protein/0.449
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.449
1v8kANPKinesin-like protein KIF2C/0.448
2e1mFADL-glutamate oxidase/0.448
2gfsPQBMitogen-activated protein kinase 14/0.448
2jdvL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
2xlsFADPutative flavin-containing monooxygenase/0.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.448
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.448
3vtbTKAVitamin D3 receptor/0.448
4iteTEYVitamin D3 receptor/0.448
4l9q9TPSerum albumin/0.448
4lb2DM5Serum albumin/0.448
1pdhFASp-hydroxybenzoate hydroxylase/0.447
1pr1FMBPurine nucleoside phosphorylase DeoD-type/0.447
2e08SAHDiphthine synthase/0.447
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.447
2g78REACellular retinoic acid-binding protein 2/0.447
2gcdSTUSerine/threonine-protein kinase TAO22.7.11.10.447
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.447
2impNAILactaldehyde dehydrogenase1.2.1.220.447
2j14GNIPeroxisome proliferator-activated receptor delta/0.447
2x23TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2ym5YM5Serine/threonine-protein kinase Chk12.7.11.10.447
3fwfCAMCamphor 5-monooxygenase1.14.15.10.447
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3jziJZLBiotin carboxylase6.3.4.140.447
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.447
4dvi2IWTankyrase-12.4.2.300.447
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.447
4l8u9AZSerum albumin/0.447
4z24FADPutative GMC-type oxidoreductase R13510.447
2xlrFADPutative flavin-containing monooxygenase/0.446
3l9mL9McAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3own3OWRenin3.4.23.150.446
3ujlA8SAbscisic acid receptor PYL2/0.446
4fgrADPPhosphoribosylaminoimidazole-succinocarboxamide synthase6.3.2.60.446
4fnyI3KALK tyrosine kinase receptor2.7.10.10.446
4h8004TAldehyde dehydrogenase, dimeric NADP-preferring/0.446
4itfTFYVitamin D3 receptor/0.446
1fvpFMANon-fluorescent flavoprotein/0.445
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1qjgEQUSteroid Delta-isomerase5.3.3.10.445
2p6kSAHDiphthine synthase/0.445
2q4wFADCytokinin dehydrogenase 71.5.99.120.445
2x7hPFNProstaglandin reductase 310.445
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.445
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.445
3ix4TX1Transcriptional activator protein LasR/0.445
4k110J9Proto-oncogene tyrosine-protein kinase Src2.7.10.20.445
1d8fSPIStromelysin-13.4.24.170.444
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1jlcFTCGag-Pol polyprotein2.7.7.490.444
1kt6RTLRetinol-binding protein 4/0.444
1o6rR19Squalene--hopene cyclase4.2.1.1290.444
1tw4CHDFatty acid-binding protein, liver/0.444
1w6yEQUSteroid Delta-isomerase5.3.3.10.444
1xzqFONtRNA modification GTPase MnmE3.6.50.444
2belCBOCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.444
3qm4PN0Cytochrome P450 2D6/0.444
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.444
5bp9SAHPutative methyltransferase protein/0.444
5emhNAPIridoid synthase1.3.1.990.444
1e3rANDSteroid Delta-isomerase5.3.3.10.443
1tlcF89Thymidylate synthase/0.443
1xdkREARetinoic acid receptor beta/0.443
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.443
2bxnIDBSerum albumin/0.443
2r0pK2CPutative FAD-monooxygenase/0.443
2vmyFFOSerine hydroxymethyltransferase/0.443
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.443
3b03VNRIsopentenyl-diphosphate delta-isomerase/0.443
3mcyZH1FimH/0.443
3vnt0JAVascular endothelial growth factor receptor 22.7.10.10.443
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.443
4bfxZVXPantothenate kinase2.7.1.330.443
4xoqF42Coenzyme F420:L-glutamate ligase/0.443
4u140HKMuscarinic acetylcholine receptor M3/0.443
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.442
1l2jETCEstrogen receptor beta/0.442
1re0AFBADP-ribosylation factor 1/0.442
1re0AFBARF guanine-nucleotide exchange factor 1/0.442
1s9dAFBCytohesin-2/0.442
1s9dAFBADP-ribosylation factor 1/0.442
2fzhDH1Dihydrofolate reductase1.5.1.30.442
2owvSAHDiphthine synthase/0.442
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.442
3fl4FL4Mitogen-activated protein kinase 14/0.442
3h3t16HCollagen type IV alpha-3-binding protein/0.442
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
3v1s0LHStrictosidine synthase4.3.3.20.442
3w0yDS4Vitamin D3 receptor/0.442
4coxIMNProstaglandin G/H synthase 21.14.99.10.442
4h3f10OBeta-secretase 13.4.23.460.442
4jkv1KSSmoothened homolog/0.442
4nka2K7Fibroblast growth factor receptor 1/0.442
4plpNADHomospermidine synthase2.5.1.440.442
5fm7ADPRuvB-like helicase/0.442
5k2cZMAAdenosine receptor A2a/0.442
1bv7XV6Gag-Pol polyprotein3.4.23.160.441
1kf6FADFumarate reductase flavoprotein subunit1.3.5.40.441
1lf3EH5Plasmepsin-23.4.23.390.441
1wbsLI2Mitogen-activated protein kinase 14/0.441
1xu9CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2pobGW4Peroxisome proliferator-activated receptor gamma/0.441
2qboCAMCamphor 5-monooxygenase1.14.15.10.441
3bqdDAYGlucocorticoid receptor/0.441
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.441
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.441
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.441
4bfzZVZPantothenate kinase2.7.1.330.441
4cf8V7HIntegrase/0.441
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.441
4nieNBHNuclear receptor ROR-gamma/0.441
4ure1PSCyclohexanol dehydrogenase/0.441
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.440
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.440
1ie8KH1Vitamin D3 receptor/0.440
1s0zEB1Vitamin D3 receptor/0.440
2fr3REACellular retinoic acid-binding protein 2/0.440
2hasC3OVitamin D3 receptor/0.440
2hcdBIVVitamin D3 receptor A/0.440
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
2zb8IMNProstaglandin reductase 21.3.1.480.440
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.440
3lfeZ84Mitogen-activated protein kinase 14/0.440
3lthUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.440
3uyk0CXProbable NDP-rhamnosyltransferase/0.440
3w5rLOAVitamin D3 receptor/0.440
4fj0HHF17beta-hydroxysteroid dehydrogenase/0.440
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4jx1CAMCamphor 5-monooxygenase1.14.15.10.440
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.440