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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
3i7g732Collagenase 33.4.24

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3i7g732Collagenase 33.4.241.000
2ow17MRMatrix metalloproteinase-93.4.24.350.626
3ljgEEFMacrophage metalloelastase3.4.24.650.619
1hy7MBSStromelysin-13.4.24.170.615
2wo8077Macrophage metalloelastase3.4.24.650.614
2hu637AMacrophage metalloelastase3.4.24.650.613
3kry3KRCollagenase 33.4.240.609
4gr8R4CMacrophage metalloelastase3.4.24.650.604
2ow06MRMatrix metalloproteinase-93.4.24.350.599
3ts4EEGMacrophage metalloelastase3.4.24.650.596
1uttCP8Macrophage metalloelastase3.4.24.650.595
3kej3EJCollagenase 33.4.240.589
3likEEGMacrophage metalloelastase3.4.24.650.589
2wo9068Macrophage metalloelastase3.4.24.650.588
4guyKLJMacrophage metalloelastase3.4.24.650.588
3lilEEAMacrophage metalloelastase3.4.24.650.586
4gqlR47Macrophage metalloelastase3.4.24.650.586
3tskQEGMacrophage metalloelastase3.4.24.650.579
2ovx4MRMatrix metalloproteinase-93.4.24.350.578
2woa576Macrophage metalloelastase3.4.24.650.577
4i03L88Macrophage metalloelastase3.4.24.650.577
3kec3KECollagenase 33.4.240.576
4gr3R45Macrophage metalloelastase3.4.24.650.576
1zvxFINNeutrophil collagenase3.4.24.340.575
1youPFDCollagenase 33.4.240.573
2d1nFA4Collagenase 33.4.240.572
1xucPB3Collagenase 33.4.240.571
2ovz5MRMatrix metalloproteinase-93.4.24.350.570
4a7b3W5Collagenase 33.4.240.570
1ztq033Collagenase 33.4.240.566
4a7b3W4Collagenase 33.4.240.563
3o2x3O2Collagenase 33.4.240.560
1g49111Stromelysin-13.4.24.170.546
1caqDPSStromelysin-13.4.24.170.540
4h7610BMacrophage metalloelastase3.4.24.650.536
3i7i518Collagenase 33.4.240.534
2yig5ELCollagenase 33.4.240.533
4g9lNGHStromelysin-13.4.24.170.533
1c8tTR1Stromelysin-13.4.24.170.530
1cizDPSStromelysin-13.4.24.170.528
1g05BBHStromelysin-13.4.24.170.527
1zs0EINNeutrophil collagenase3.4.24.340.527
2d1oFA4Stromelysin-13.4.24.170.524
4gr0R4BMacrophage metalloelastase3.4.24.650.524
1slnINHStromelysin-13.4.24.170.521
1b8yIN7Stromelysin-13.4.24.170.520
1hovI5272 kDa type IV collagenase3.4.24.240.514
1d8fSPIStromelysin-13.4.24.170.511
1hv5RXPStromelysin-33.4.240.509
1xurPB5Collagenase 33.4.240.507
4ja1NGHStromelysin-13.4.24.170.500
4dpeNGHStromelysin-13.4.24.170.498
1g4kHQQStromelysin-13.4.24.170.492
4b8wNAPGDP-L-fucose synthase1.1.1.2710.491
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.490
2ow28MRMatrix metalloproteinase-93.4.24.350.488
1d8mBBHStromelysin-13.4.24.170.487
2oxwILE_ALA_GLYMacrophage metalloelastase3.4.24.650.485
4fco0U4Beta-secretase 13.4.23.460.483
5dbfNDPIridoid synthase1.3.1.990.482
3cukFADD-amino-acid oxidase1.4.3.30.481
1bzsBSINeutrophil collagenase3.4.24.340.480
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.480
1xkqNDPUncharacterized protein/0.478
4lxa1YSBeta-secretase 13.4.23.460.478
1bqoN25Stromelysin-13.4.24.170.477
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.476
2pobGW4Peroxisome proliferator-activated receptor gamma/0.475
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.475
3oqfS51Renin3.4.23.150.473
3zxhE41Collagenase 33.4.240.473
4d89BXDBeta-secretase 13.4.23.460.473
3b6zCO7Enoyl reductase LovC10.472
4h3i10VBeta-secretase 13.4.23.460.472
1yqxNAPSinapyl alcohol dehydrogenase/0.471
2y6dTQJMatrilysin3.4.24.230.471
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.470
3vg10GTBeta-secretase 13.4.23.460.470
4dh60KNBeta-secretase 13.4.23.460.470
2w0dCGSMacrophage metalloelastase3.4.24.650.469
5hsaFASAlcohol oxidase 11.1.3.130.469
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.468
3bg7FADPyranose 2-oxidase/0.468
3qofGDPAtlastin-13.6.50.468
4b79NADProbable short-chain dehydrogenase/0.468
4dpf0LGBeta-secretase 13.4.23.460.468
2woa023Macrophage metalloelastase3.4.24.650.466
4dlbNADS-(hydroxymethyl)glutathione dehydrogenase/0.466
2fzwNADAlcohol dehydrogenase class-31.1.1.10.465
3toxNAPPutative oxidoreductase/0.465
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.465
1n5dNDPCarbonyl reductase [NADPH] 1/0.464
1sozVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.464
2y0mACOHistone acetyltransferase KAT8/0.464
3vyfVYFRenin3.4.23.150.464
5emhNAPIridoid synthase1.3.1.990.464
1d7xSPCStromelysin-13.4.24.170.463
2xlsFADPutative flavin-containing monooxygenase/0.463
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.463
3lpjZ75Beta-secretase 13.4.23.460.462
4ewo996Beta-secretase 13.4.23.460.462
1yqdNAPSinapyl alcohol dehydrogenase/0.461
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
4dpi0N1Beta-secretase 13.4.23.460.461
4qecNAPElxO/0.461
4yagNAIC alpha-dehydrogenase/0.461
1xseNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
2getCOKPantothenate kinase2.7.1.330.460
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.460
3vucHHERenin3.4.23.150.460
4frkDWDBeta-secretase 13.4.23.460.460
3dv5BAVBeta-secretase 13.4.23.460.459
3lqfNADGalactitol dehydrogenase/0.459
4oztP1AEcdysone receptor, putative/0.459
1xe55FEPlasmepsin-23.4.23.390.458
1yb5NAPQuinone oxidoreductase1.6.5.50.458
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.458
2z3lPHE_ARG_TYR_LEU_GLYLeucyl/phenylalanyl-tRNA--protein transferase2.3.2.60.458
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.458
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.458
3k5gBJCBeta-secretase 13.4.23.460.458
4an4DUDPutative glycosyl transferase/0.458
4b8zNAPGDP-L-fucose synthase1.1.1.2710.458
4d04FADPhenylacetone monooxygenase1.14.13.920.458
4egbNADdTDP-glucose 4,6-dehydratase/0.458
1wntNAPL-xylulose reductase1.1.1.100.457
2g1r3IGRenin3.4.23.150.457
3pqbVGPPutative oxidoreductase/0.457
4dc1NDPPutative ketoacyl reductase1.3.10.457
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.457
5dbgNADIridoid synthase1.3.1.990.457
1ae1NAPTropinone reductase 1/0.456
2c20NADUDP-glucose 4-epimerase/0.456
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.456
3to6LYS_CMCHistone acetyltransferase ESA1/0.456
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.456
4impNDPPolyketide synthase extender modules 3-4/0.456
4nbwNADShort-chain dehydrogenase/reductase SDR/0.456
6ctsCICCitrate synthase, mitochondrial2.3.3.10.456
1fwmCB3Thymidylate synthase/0.455
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.455
2p5uNADUDP-glucose 4-epimerase/0.455
2v16C47Renin3.4.23.150.455
3qlrNDPDihydrofolate reductase1.5.1.30.455
1bim0QBRenin3.4.23.150.454
1mjbACOHistone acetyltransferase ESA1/0.454
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
2wo8023Macrophage metalloelastase3.4.24.650.454
3vf30GSBeta-secretase 13.4.23.460.454
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.454
2g78REACellular retinoic acid-binding protein 2/0.453
2ifaFMNUncharacterized protein/0.453
2ignFADPyranose 2-oxidase/0.453
2z1qFADAcyl-CoA dehydrogenase/0.453
2zfnACOHistone acetyltransferase RTT1092.3.1.480.453
3ecg065Gag-Pol polyprotein3.4.23.470.453
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.453
3up0D7SaceDAF-12/0.453
4l4xNDPAmphI/0.453
5dcyNAPIridoid synthase1.3.1.990.453
1rneC60Renin3.4.23.150.452
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.452
2ou2ACOHistone acetyltransferase KAT5/0.452
2v13C40Renin3.4.23.150.452
2wf4ZY4Beta-secretase 13.4.23.460.452
3jw2017Gag-Pol polyprotein3.4.23.160.452
3k5c0BIBeta-secretase 13.4.23.460.452
3ohoZ79Stromelysin-13.4.24.170.452
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
4bftZVTPantothenate kinase2.7.1.330.452
4bixADPSensor histidine kinase CpxA/0.452
4dx9SER_ALA_VAL_THRIntegrin beta-1/0.452
4dx9SER_ALA_VAL_THRIntegrin beta-1-binding protein 1/0.452
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.452
1gcoNADGlucose 1-dehydrogenase1.1.1.470.451
2hpsCTZCa2+-triggered coelenterazine-binding protein 1/0.451
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.451
3tdaPN0Cytochrome P450 2D6/0.451
4at0FADPossible succinate dehydrogenase/0.451
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
5af7FADAcyl-CoA dehydrogenase/0.451
2xlrFADPutative flavin-containing monooxygenase/0.450
3etdNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.450
3own3OWRenin3.4.23.150.450
3syiFADSulfide-quinone reductase/0.450
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.450
4ambDUDPutative glycosyl transferase/0.450
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.450
1cydNDPCarbonyl reductase [NADPH] 21.1.1.1840.449
1geeNADGlucose 1-dehydrogenase1.1.1.470.449
1rwbNADGlucose 1-dehydrogenase1.1.1.470.449
1trgCB3Thymidylate synthase/0.449
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.449
2iw5FADLysine-specific histone demethylase 1A10.449
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.449
2xvfFADPutative flavin-containing monooxygenase/0.449
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.449
3cosNADAlcohol dehydrogenase 41.1.1.10.449
3lpkZ76Beta-secretase 13.4.23.460.449
4ejmNAPPutative zinc-binding dehydrogenase/0.449
4j7uNAPSepiapterin reductase1.1.1.1530.449
1blzACVIsopenicillin N synthase1.21.3.10.448
1e3eNAIAlcohol dehydrogenase 41.1.1.10.448
1pr9NAPL-xylulose reductase1.1.1.100.448
1zemNADXylitol dehydrogenase/0.448
2givACOHistone acetyltransferase KAT8/0.448
2i4qUA4Renin3.4.23.150.448
2rjp886A disintegrin and metalloproteinase with thrombospondin motifs 43.4.24.820.448
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.448
1biwS80Stromelysin-13.4.24.170.447
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.447
1o97FADElectron transfer flavoprotein subunit alpha/0.447
1xs7MMIBeta-secretase 13.4.23.460.447
2pg0FADAcyl-CoA dehydrogenase/0.447
3ge6FMNNitroreductase/0.447
3kpkFADSulfide-quinone reductase/0.447
3q33ACOHistone acetyltransferase RTT1092.3.1.480.447
4dmmNAP3-oxoacyl-[acyl-carrier-protein] reductase/0.447
4fr4STUSerine/threonine-protein kinase 32A2.7.11.10.447
4j0v1H7Beta-secretase 13.4.23.460.447
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.447
1cf3FADGlucose oxidase1.1.3.40.446
1ja0FMNNADPH--cytochrome P450 reductase/0.446
1mjaCOAHistone acetyltransferase ESA1/0.446
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.446
1w4xFADPhenylacetone monooxygenase1.14.13.920.446
1w6hTITPlasmepsin-23.4.23.390.446
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
2b3dFADModulator of drug activity B/0.446
2ftoCB3Thymidylate synthase/0.446
2ylrFADPhenylacetone monooxygenase1.14.13.920.446
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.446
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.446
3q43D66M1 family aminopeptidase3.4.110.446
3r7kFDAProbable acyl CoA dehydrogenase/0.446
3slz3TLPutative gag-pro-pol polyprotein/0.446
4exg916Beta-secretase 13.4.23.460.446
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.446
1di8DTQCyclin-dependent kinase 22.7.11.220.445
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.445
1mv8GDXGDP-mannose 6-dehydrogenase1.1.1.1320.445
1pqc444Oxysterols receptor LXR-beta/0.445
1tehNADAlcohol dehydrogenase class-31.1.1.10.445
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.445
2bfqAR6[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.445
2po7CHDFerrochelatase, mitochondrial4.99.1.10.445
2qn7HBZGlycogen phosphorylase, muscle form2.4.1.10.445
2wesFADTryptophan 5-halogenase/0.445
3aw9NADNAD-dependent epimerase/dehydratase/0.445
3cid318Beta-secretase 13.4.23.460.445
3eksCY9Actin-5C/0.445
3fpzAHZThiamine thiazole synthase/0.445
3gqvNAPEnoyl reductase LovC10.445
3gy0NAPNAD(P)-dependent oxidoreductase/0.445
3lsmSFDPyranose 2-oxidase/0.445
3s3r0IWCathepsin B-like peptidase (C01 family)/0.445
3sz0FADSulfide-quinone reductase/0.445
3vsxR32Renin3.4.23.150.445
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.445
4tm0NAPKtzI/0.445
5jlaNADPutative short-chain dehydrogenase/reductase/0.445
1qorNDPQuinone oxidoreductase 1/0.444
2iqgF2IBeta-secretase 13.4.23.460.444
2j83BATUlilysin3.4.240.444
3bgxMEFThymidylate synthase/0.444
3ekp478Gag-Pol polyprotein3.4.23.160.444
3ixj586Beta-secretase 13.4.23.460.444
3zuyTCHTransporter/0.444
4bb3KKAIsopenicillin N synthase1.21.3.10.444
4bfxZVXPantothenate kinase2.7.1.330.444
4esoNAPPutative oxidoreductase/0.444
4j7xNAPSepiapterin reductase1.1.1.1530.444
1drfFOLDihydrofolate reductase1.5.1.30.443
1honGNHAdenylosuccinate synthetase/0.443
1ppjANYCytochrome b/0.443
2jb4A14Isopenicillin N synthase1.21.3.10.443
3ohh3HHBeta-secretase 13.4.23.460.443
3t14FADSulfide-quinone reductase/0.443
4l7j1W2Beta-secretase 13.4.23.460.443
4yryFADGlutamate synthase, beta subunit/0.443
5idwNAPShort-chain dehydrogenase/reductase SDR/0.443
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.442
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.442
2g1y5IGRenin3.4.23.150.442
2g8yNADHydroxycarboxylate dehydrogenase B/0.442
2gevCOKPantothenate kinase2.7.1.330.442
2iko7IGRenin3.4.23.150.442
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.442
2p83MR0Beta-secretase 13.4.23.460.442
3cyw017Gag-Pol polyprotein3.4.23.160.442
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.442
3jynNDPQuinone oxidoreductase/0.442
3l5dBDVBeta-secretase 13.4.23.460.442
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.442
3p4tFAOPutative acyl-CoA dehydrogenase/0.442
3p6oETGCamphor 5-monooxygenase1.14.15.10.442
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.442
3vswR31Renin3.4.23.150.442
3w8dNAD3-hydroxybutyrate dehydrogenase/0.442
4fx9FADCoenzyme A disulfide reductase1.8.1.140.442
4gl4NAIAlcohol dehydrogenase class-3/0.442
4n6bCOAUncharacterized protein/0.442
4yaiNAIC alpha-dehydrogenase/0.442
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.442
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
2r0cFADPutative FAD-monooxygenase/0.441
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.441
3ru7NADUDP-N-acetylglucosamine 4-epimerase/0.441
3ruhNADUDP-N-acetylglucosamine 4-epimerase/0.441
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.441
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.441
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.441
5dbjFADFADH2-dependent halogenase PltA/0.441
1eveE20Acetylcholinesterase3.1.1.70.440
1g1aNADdTDP-glucose 4,6-dehydratase/0.440
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.440
1luaNAPBifunctional protein MdtA1.5.1.50.440
1mp0NADAlcohol dehydrogenase class-31.1.1.10.440
1w4zNAPPutative ketoacyl reductase1.3.10.440
1x7hNDPPutative ketoacyl reductase1.3.10.440
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.440
2ebaFADPutative glutaryl-CoA dehydrogenase/0.440
2hq9FADMll6688 protein/0.440
2oy2ILE_ALA_GLYNeutrophil collagenase3.4.24.340.440
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.440
2vkmBSDBeta-secretase 13.4.23.460.440
2wf1ZY1Beta-secretase 13.4.23.460.440
2ylsFADPhenylacetone monooxygenase1.14.13.920.440
2yutNAPPutative short-chain oxidoreductase/0.440
3cluFADElectron transfer flavoprotein subunit alpha/0.440
3gwdFADCyclohexanone monooxygenase/0.440
3he3FADUDP-galactopyranose mutase/0.440
3hekBD0Heat shock protein HSP 90-alpha/0.440
3qaaG04Gag-Pol polyprotein3.4.23.160.440
3qvpFADGlucose oxidase1.1.3.40.440
3t2zFADSulfide-quinone reductase/0.440
4mdhNADMalate dehydrogenase, cytoplasmic1.1.1.370.440
4qi7FADCellobiose dehydrogenase/0.440
4tlxFDAKtzI/0.440
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.440