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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
3l71AZOCytochrome b

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3l71AZOCytochrome b/1.000
3tguWF3Cytochrome b/0.713
3l70JZVCytochrome b/0.624
1sqpMYXCytochrome b/0.600
1sqbAZOCytochrome b/0.594
3h1jSMACytochrome b/0.515
1q5dEPBEpothilone C/D epoxidase1.140.507
3p9tTCLRepressor/0.501
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.498
4nc3ERM5-hydroxytryptamine receptor 2B/0.498
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.498
4iaq2GM5-hydroxytryptamine receptor 1B/0.496
2dqsTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.493
4iarERM5-hydroxytryptamine receptor 1B/0.493
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.492
4ib4ERM5-hydroxytryptamine receptor 2B/0.489
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.488
1tduCB3Thymidylate synthase/0.487
4klaCHDFerrochelatase, mitochondrial4.99.1.10.487
2agvTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.486
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.485
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.485
3abaFLICytochrome P450/0.484
1zg32HIIsoflavone 4'-O-methyltransferase/0.482
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.482
1ppjSMACytochrome b/0.480
4j6bPLOCytochrome P450 monooxygenase/0.480
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.479
1jutLYDThymidylate synthase/0.478
3bfa9ODOdorant binding protein ASP1/0.478
5bn3ADPV-type ATP synthase alpha chain/0.478
5bn3ADPNEQ263/0.478
4j6cSTRCytochrome P450 monooxygenase/0.477
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.476
3ar7TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.476
2vcmM11Isopenicillin N synthase1.21.3.10.475
1xuoLA1Integrin alpha-L/0.474
1xdsDRAAclacinomycin 10-hydroxylase RdmB4.1.10.473
2h42VIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.473
1pp9SMACytochrome b/0.471
5k2bZMAAdenosine receptor A2a/0.471
1ddtAPUDiphtheria toxin/0.470
1yinCM3Estrogen receptor/0.469
1ysx4EBSerum albumin/0.469
4dvq1CACytochrome P450 11B2, mitochondrial1.14.15.40.469
1w06W05Isopenicillin N synthase1.21.3.10.468
2ftoCB3Thymidylate synthase/0.468
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.468
2y60M8FIsopenicillin N synthase1.21.3.10.467
3cv9VDXVitamin D3 dihydroxylase/0.467
3hywDCQSulfide-quinone reductase/0.467
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.467
1lriCLRBeta-elicitin cryptogein/0.466
3is9AC7Gag-Pol polyprotein2.7.7.490.466
3p99LNPLanosterol 14-alpha-demethylase/0.466
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.466
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.465
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.465
2z3uCRRCytochrome P450/0.465
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.465
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.465
3nalDBKCalcium-transporting ATPase/0.465
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.464
3t8xT8XT-cell surface glycoprotein CD1b/0.464
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.463
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.463
3a1l2CCCytochrome P450/0.463
3zkyWT4Isopenicillin N synthase1.21.3.10.463
3zoiM2WIsopenicillin N synthase1.21.3.10.463
4h4o506Gag-Pol polyprotein2.7.7.490.463
4jlj1NMDeoxycytidine kinase2.7.1.740.463
1iyzNDPProbable quinone oxidoreductase/0.462
1pkfEPDEpothilone C/D epoxidase1.140.462
2aibERGBeta-elicitin cinnamomin/0.462
3ctj320Hepatocyte growth factor receptor2.7.10.10.462
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
3p3zP3ZPutative cytochrome P450/0.462
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.462
4j6dTESCytochrome P450 monooxygenase/0.462
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.462
5uviZMAAdenosine receptor A2a/0.462
2b00GCHPhospholipase A2, major isoenzyme3.1.1.40.461
2bxnIDBSerum albumin/0.461
2cl5BIECatechol O-methyltransferase2.1.1.60.461
3td8D2RDihydrofolate reductase1.5.1.30.461
4qa0SHHHistone deacetylase 83.5.1.980.461
1fmlRTLRetinol dehydratase/0.460
1fp1HCCIsoliquiritigenin 2'-O-methyltransferase/0.460
1m79MQ1Dihydrofolate reductase1.5.1.30.460
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.460
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.460
1bk0ACVIsopenicillin N synthase1.21.3.10.459
1blzACVIsopenicillin N synthase1.21.3.10.459
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.459
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.459
3irxUDRGag-Pol polyprotein2.7.7.490.459
3nwlNDPCatalase1.11.1.60.459
4r20AERCytochrome P450 family 17 polypeptide 2/0.459
3uzcT4EAdenosine receptor A2a/0.459
1eioGCHGastrotropin/0.458
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
1rdtL79Retinoic acid receptor RXR-alpha/0.458
2b378PSEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.458
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
2hm9TRRDihydrofolate reductase1.5.1.30.458
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
5d1bTSNHistone deacetylase 83.5.1.980.458
1ek2CDUBifunctional epoxide hydrolase 2/0.457
1hb3SCVIsopenicillin N synthase1.21.3.10.457
2w4qCBWProstaglandin reductase 21.3.1.480.457
3bqdDAYGlucocorticoid receptor/0.457
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
4jdaA9SAbscisic acid receptor PYL3/0.457
5jtbZMAAdenosine receptor A2a/0.457
1l2jETCEstrogen receptor beta/0.456
1s0xC3SNuclear receptor ROR-alpha/0.456
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.456
3g70A5TRenin3.4.23.150.456
4h4m494Gag-Pol polyprotein2.7.7.490.456
3reyXACAdenosine receptor A2a/0.456
2qjySMACytochrome b/0.455
2vbpVB1Isopenicillin N synthase1.21.3.10.455
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.455
3dl9V2HVitamin D 25-hydroxylase/0.455
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
3qm4PN0Cytochrome P450 2D6/0.455
4ubsDIFPentalenic acid synthase1.14.15.110.455
5k2cZMAAdenosine receptor A2a/0.455
5k2aZMAAdenosine receptor A2a/0.455
3p6nDSOCamphor 5-monooxygenase1.14.15.10.454
3pm0BHFCytochrome P450 1B1/0.454
4at0FADPossible succinate dehydrogenase/0.454
4jbtASDCytochrome P450 monooxygenase/0.454
4jqh1MFAlr2278 protein/0.454
4lb2DM5Serum albumin/0.454
1w22NHBHistone deacetylase 83.5.1.980.453
2jedLG8Protein kinase C theta type2.7.11.130.453
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
3drcMTXDihydrofolate reductase1.5.1.30.453
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.453
3emlZMAAdenosine receptor A2a/0.453
1ezvSMACytochrome b/0.452
1xddAAYIntegrin alpha-L/0.452
2ntvP1HEnoyl-[acyl-carrier-protein] reductase [NADH]/0.452
2qjpSMACytochrome b/0.452
3jynNDPQuinone oxidoreductase/0.452
3lu8IQXSerum albumin/0.452
3vg9ZMAAdenosine receptor A2a/0.452
4boeCLRJapanin/0.452
1hb1OCVIsopenicillin N synthase1.21.3.10.451
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.451
1kzjCB3Thymidylate synthase/0.451
1yc2NADNAD-dependent protein deacylase 2/0.451
2bu9HFVIsopenicillin N synthase1.21.3.10.451
2ibzSMACytochrome b/0.451
2p7zOHTEstrogen-related receptor gamma/0.451
2w0bCMWLanosterol 14-alpha demethylase1.14.13.700.451
3p6oETGCamphor 5-monooxygenase1.14.15.10.451
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
4qe6JN3Bile acid receptor/0.451
2uxoTACHTH-type transcriptional regulator TtgR/0.450
3g4lROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3tk3CPZCytochrome P450 2B41.14.14.10.450
4equG6ISerine/threonine-protein kinase 102.7.11.10.450
5bp9SAHPutative methyltransferase protein/0.450
1diuBDMDihydrofolate reductase1.5.1.30.449
1jtqLY3Thymidylate synthase/0.449
1rf9DBRCamphor 5-monooxygenase1.14.15.10.449
1zprCB3Thymidylate synthase/0.449
2b5j3ACGag-Pol polyprotein2.7.7.490.449
3htjETEbrA repressor/0.449
3lalKRVGag-Pol polyprotein2.7.7.490.449
4ddrMMVDihydrofolate reductase1.5.1.30.449
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.449
4hyf1AKTankyrase-22.4.2.300.449
4knzCB3Thymidylate synthase/0.449
4rbs0RVMetallo-beta-lactamase type 2/0.449
1hk3T44Serum albumin/0.448
1ly4COQDihydrofolate reductase1.5.1.30.448
1o6rR19Squalene--hopene cyclase4.2.1.1290.448
2c7xNRBCytochrome P450 monooxygenase PikC/0.448
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.448
3tmz06XCytochrome P450 2B41.14.14.10.448
4o761M3Bromodomain-containing protein 4/0.448
3rfmCFFAdenosine receptor A2a/0.448
1dhjMTXDihydrofolate reductase1.5.1.30.447
1kb9SMACytochrome b/0.447
1oc1ASVIsopenicillin N synthase1.21.3.10.447
1sj0E4DEstrogen receptor/0.447
1tg56454-hydroxyphenylpyruvate dioxygenase1.13.11.270.447
1ygkRRCPyridoxal kinase2.7.1.350.447
2jb4A14Isopenicillin N synthase1.21.3.10.447
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.447
3zsh469Mitogen-activated protein kinase 14/0.447
4ea2RWZDehydrosqualene synthase/0.447
4i2pG73Gag-Pol polyprotein2.7.7.490.447
1f4fTP3Thymidylate synthase/0.446
1osvCHCBile acid receptor/0.446
1tw2ERTCarminomycin 4-O-methyltransferase DnrK2.1.1.2920.446
1vj3TABDihydrofolate reductase1.5.1.30.446
1zhwHC2Oxysterol-binding protein homolog 4/0.446
2fmn4HF5,10-methylenetetrahydrofolate reductase1.5.1.200.446
2g2hP16Tyrosine-protein kinase ABL12.7.10.20.446
2yncYNCGlycylpeptide N-tetradecanoyltransferase/0.446
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.446
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.446
1dnaCB3Thymidylate synthase/0.445
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1ia1TQ3Dihydrofolate reductase1.5.1.30.445
1nceCB3Thymidylate synthase/0.445
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3fkoFKOMitogen-activated protein kinase 14/0.445
3tdaPN0Cytochrome P450 2D6/0.445
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
4b4w9L9Bifunctional protein FolD/0.445
4bfpSWYTankyrase-22.4.2.300.445
4cd2FOLDihydrofolate reductase1.5.1.30.445
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.445
4ia7BIVVitamin D3 receptor A/0.445
1fwmCB3Thymidylate synthase/0.444
1re9DSOCamphor 5-monooxygenase1.14.15.10.444
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.444
1yhjR6CPyridoxal kinase2.7.1.350.444
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.444
3k3bADPKinesin-like protein KIF11/0.444
3p6pA6BCamphor 5-monooxygenase1.14.15.10.444
3v94WYQPhosphodiesterase/0.444
3vjcZGASqualene synthase2.5.1.210.444
3w5p4OAVitamin D3 receptor/0.444
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4h9614QDihydrofolate reductase1.5.1.30.444
4i8vBHFCytochrome P450 1A11.14.14.10.444
4nieNBHNuclear receptor ROR-gamma/0.444
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.444
3uzaT4GAdenosine receptor A2a/0.444
1aoeGW3Dihydrofolate reductase1.5.1.30.443
1fmjRTLRetinol dehydratase/0.443
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.443
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.443
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.443
2rqfJH3Hemolymph juvenile hormone binding protein/0.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
3cx5SMACytochrome b/0.443
3e5aVX6Aurora kinase A2.7.11.10.443
4l5b1UXDeoxycytidine kinase2.7.1.740.443
3pwhZMAAdenosine receptor A2a/0.443
1ly3COGDihydrofolate reductase1.5.1.30.442
1ppjANYCytochrome b/0.442
1qiqACCIsopenicillin N synthase1.21.3.10.442
1upw444Oxysterols receptor LXR-beta/0.442
2fdyD4GCytochrome P450 2A61.14.130.442
2hasC3OVitamin D3 receptor/0.442
2qimZEAClass 10 plant pathogenesis-related protein/0.442
2w98P1ZProstaglandin reductase 21.3.1.480.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
2yiuSMACytochrome b/0.442
3bgxMEFThymidylate synthase/0.442
3bhrTHGThymidylate synthase/0.442
3lakKR1Gag-Pol polyprotein2.7.7.490.442
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
3p6mDSOCamphor 5-monooxygenase1.14.15.10.442
3vt8YI3Vitamin D3 receptor/0.442
4elb34SDihydrofolate reductase/0.442
4g1qT27Gag-Pol polyprotein2.7.7.490.442
1al8DHPPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.441
1dgbNDPCatalase1.11.1.60.441
1uzwCDHIsopenicillin N synthase1.21.3.10.441
1xp6AIUEstrogen receptor/0.441
1yqj6NPMitogen-activated protein kinase 14/0.441
2wo7ASVIsopenicillin N synthase1.21.3.10.441
2wpwACOOrf14/0.441
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3dmjGWEPol protein/0.441
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
3qlhT27Gag-Pol polyprotein2.7.7.490.441
3qlrQLRDihydrofolate reductase1.5.1.30.441
3uvvREARetinoic acid receptor RXR-alpha/0.441
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
4ele31IDihydrofolate reductase/0.441
4k4eK4ETankyrase-12.4.2.300.441
4o701QKBromodomain-containing protein 4/0.441
5iu86DZAdenosine receptor A2a/0.441
1errRALEstrogen receptor/0.440
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.440
2q9fC3SCholesterol 24-hydroxylase/0.440
2y02Y01Beta-1 adrenergic receptor/0.440
3thrC2FGlycine N-methyltransferase2.1.1.200.440
3uftHW7Nitric oxide synthase, brain1.14.13.390.440
3uwlFOZThymidylate synthase/0.440
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440