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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
2yg6FADPutrescine oxidase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2yg6FADPutrescine oxidase/1.000
3rhaFDAPutrescine oxidase/0.612
2jb2FADL-amino acid oxidase/0.560
2jb1FADL-amino acid oxidase/0.553
2yg7FADPutrescine oxidase/0.548
4echFADPolyamine oxidase FMS1/0.547
1reoFADL-amino-acid oxidase1.4.3.20.543
2y48FADLysine-specific histone demethylase 1A10.539
3cntFADPolyamine oxidase FMS1/0.538
4fwjFADLysine-specific histone demethylase 1B10.530
5l3dFADLysine-specific histone demethylase 1A10.530
3cn8FADPolyamine oxidase FMS1/0.526
3nn6FB06-hydroxy-L-nicotine oxidase/0.521
1yy5FADPolyamine oxidase FMS1/0.512
3kpfFADPolyamine oxidase1.5.3.140.505
4i58FADCyclohexylamine Oxidase/0.502
1xpqFADPolyamine oxidase FMS1/0.501
1tdkFADL-amino-acid oxidase1.4.3.20.497
1f8rFADL-amino-acid oxidase1.4.3.20.496
3lshFADPyranose 2-oxidase/0.496
1f3pFADFerredoxin reductase/0.495
3q71AR6Poly [ADP-ribose] polymerase 142.4.2.300.495
3k4cFADPyranose 2-oxidase/0.492
5g3tFDAFlavin-dependent L-tryptophan oxidase VioA/0.492
1ryiFADGlycine oxidase1.4.3.190.488
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.487
4yaiNAIC alpha-dehydrogenase/0.485
1tdoFADL-amino-acid oxidase1.4.3.20.484
3l8kADPDihydrolipoamide dehydrogenase (PdhD-3)/0.484
3if9FADGlycine oxidase1.4.3.190.483
3k7tFAD6-hydroxy-L-nicotine oxidase/0.483
1tdnFADL-amino-acid oxidase1.4.3.20.480
4ntdFADThioredoxin reductase/0.480
4h4yFADBiphenyl dioxygenase ferredoxin reductase subunit/0.479
4l4xNDPAmphI/0.479
2c3cFAD2-oxopropyl-CoM reductase, carboxylating1.8.1.50.475
4udqFAD5-(hydroxymethyl)furfural oxidase/0.475
3nxxNDPDihydrofolate reductase1.5.1.30.474
4yshFADGlycine oxidase/0.474
3oafOAGDihydrofolate reductase1.5.1.30.473
1ipeNDPTropinone reductase 21.1.1.2360.472
2babFADPutative aminooxidase/0.472
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.472
2yr4FADPhenylalanine 2-monooxygenase precursor1.13.12.90.472
1i8tFADUDP-galactopyranose mutase5.4.99.90.471
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.471
3q9tFAYUncharacterized protein/0.471
4uirFADOleate hydratase4.2.1.530.470
2b9wFADPutative aminooxidase/0.469
3vdqNAD3-hydroxybutyrate dehydrogenase/0.469
5bsgNAPPyrroline-5-carboxylate reductase/0.469
2cvjFADThioredoxin reductase related protein/0.468
2yy7NADL-threonine dehydrogenase/0.468
4ykgNADAlkyl hydroperoxide reductase subunit F1.8.10.468
5g3sFDAFlavin-dependent L-tryptophan oxidase VioA/0.467
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.466
4yntFDAGlucose oxidase, putative/0.466
5lc1NADL-threonine 3-dehydrogenase/0.466
1ae1NAPTropinone reductase 1/0.465
1getFADGlutathione reductase1.8.1.70.465
3q43D66M1 family aminopeptidase3.4.110.465
4bmvNAPShort-chain dehydrogenase/0.465
2ydxNAPMethionine adenosyltransferase 2 subunit beta/0.464
3kveFADL-amino-acid oxidase/0.464
3lsiFADPyranose 2-oxidase/0.464
2zzcFADThioredoxin reductase 1, cytoplasmic1.8.1.90.463
3d84NDPDihydrofolate reductase1.5.1.30.463
3s3vTOPDihydrofolate reductase1.5.1.30.463
4ajp88NL-lactate dehydrogenase A chain1.1.1.270.463
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.463
4h4rFADBiphenyl dioxygenase ferredoxin reductase subunit/0.463
4udrFAD5-(hydroxymethyl)furfural oxidase/0.463
5c2tFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.463
3axbFADPutative oxidoreductase/0.462
1jqiFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.461
1ng3FADGlycine oxidase1.4.3.190.461
1d4dFADFumarate reductase flavoprotein subunit1.3.5.40.460
1psdNADD-3-phosphoglycerate dehydrogenase1.1.1.950.460
3lzwFADFerredoxin--NADP reductase 21.18.1.20.460
1w4xFADPhenylacetone monooxygenase1.14.13.920.459
3fpzAHZThiamine thiazole synthase/0.459
1rp0AHZThiamine thiazole synthase, chloroplastic/0.458
2rgoFADAlpha-Glycerophosphate Oxidase/0.458
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.458
1feaFADTrypanothione reductase1.8.1.120.457
1nqoNADGlyceraldehyde-3-phosphate dehydrogenase/0.457
1snyNAPLD36273p/0.457
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.457
3qwbNDPProbable quinone oxidoreductase1.6.5.50.457
4mo2FADUDP-galactopyranose mutase/0.457
1geuFADGlutathione reductase1.8.1.70.456
1v0jFADUDP-galactopyranose mutase5.4.99.90.456
1ve9FADD-amino-acid oxidase1.4.3.30.456
1w6hTITPlasmepsin-23.4.23.390.456
2b9yFADPutative aminooxidase/0.456
2v3aFADRubredoxin-NAD(+) reductase1.18.1.10.456
3l9hEMQKinesin-like protein KIF11/0.456
3w8eNAD3-hydroxybutyrate dehydrogenase/0.456
5iqiGNPBifunctional AAC/APH2.3.10.456
1d4cFADFumarate reductase flavoprotein subunit1.3.5.40.455
1gegNADDiacetyl reductase [(S)-acetoin forming]1.1.1.3040.455
1trbFADThioredoxin reductase1.8.1.90.455
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.455
1lquFADNADPH-ferredoxin reductase FprA1.18.1.20.454
1osvCHCBile acid receptor/0.454
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.454
2zynBCDPeriplasmic binding protein/0.454
3k7mFAD6-hydroxy-L-nicotine oxidase/0.454
4xq9NADHomospermidine synthase2.5.1.440.454
2bi7FADUDP-galactopyranose mutase5.4.99.90.453
2ozuACOHistone acetyltransferase KAT6A/0.453
3eluSAMMethyltransferase/0.453
4g95OAGDihydrofolate reductase1.5.1.30.453
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.452
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
3lsmSFDPyranose 2-oxidase/0.452
4b4w9L9Bifunctional protein FolD/0.452
4d5gFADCyclohexane-1,2-dione hydrolase3.7.1.110.452
4m10ICDProstaglandin G/H synthase 21.14.99.10.452
4qi5FADCellobiose dehydrogenase/0.452
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
4y9lFADAcyl-CoA dehydrogenase family member 11/0.452
5jscFADPutative acyl-CoA dehydrogenase/0.452
1m75CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.451
2bacFADPutative aminooxidase/0.451
2q0lFADThioredoxin reductase1.8.1.90.451
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.451
3qlsNDPDihydrofolate reductase1.5.1.30.451
4ajo88NL-lactate dehydrogenase A chain1.1.1.270.451
4h4tFADBiphenyl dioxygenase ferredoxin reductase subunit/0.451
4h4zFADBiphenyl dioxygenase ferredoxin reductase subunit/0.451
1c1dNAIPhenylalanine dehydrogenase/0.450
1f20NAPNitric oxide synthase, brain1.14.13.390.450
1wc3APCAdenylate cyclase/0.450
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
4pd6URINucleoside permease/0.450
5br7FADUDP-galactopyranose mutase/0.450
1e1kFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.449
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.449
1t2aNDPGDP-mannose 4,6 dehydratase4.2.1.470.449
1zmdNAIDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.449
2prbCOAAminoglycoside 6-N-acetyltransferase type Ib11/0.449
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.449
3hdyFADUDP-galactopyranose mutase/0.449
3vqrFADPutative oxidoreductase/0.449
4fn4NADShort chain dehydrogenase/0.449
5c3jFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.449
5kczNAJAlcohol dehydrogenase E chain1.1.1.10.449
1zmdFADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.448
2ba9FADPutative aminooxidase/0.448
2npxFADNADH peroxidase1.11.1.10.448
2wdzNADGalactitol dehydrogenase/0.448
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
2ylrFADPhenylacetone monooxygenase1.14.13.920.448
3eksCY9Actin-5C/0.448
4mihFADPyranose 2-oxidase1.1.3.100.448
4mo2FDAUDP-galactopyranose mutase/0.448
1pd9CO4Dihydrofolate reductase1.5.1.30.447
1rrmAPRLactaldehyde reductase1.1.1.770.447
1zemNADXylitol dehydrogenase/0.447
2w9hTOPDihydrofolate reductase1.5.1.30.447
3m13FADMonomeric sarcosine oxidase1.5.3.10.447
3mqe416Prostaglandin G/H synthase 21.14.99.10.447
3v2bAR6Poly [ADP-ribose] polymerase 152.4.2.300.447
3vs1VSATyrosine-protein kinase HCK2.7.10.20.447
4i02CMPcAMP-activated global transcriptional regulator CRP/0.447
4m11MXMProstaglandin G/H synthase 21.14.99.10.447
4rdiATPtRNA threonylcarbamoyladenosine dehydratase6.10.447
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.446
1iy8NADLevodione reductase/0.446
1l7eNAINAD(P) transhydrogenase subunit alpha part 11.6.1.20.446
1tdfFADThioredoxin reductase1.8.1.90.446
2eq7FADDihydrolipoyl dehydrogenase/0.446
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.446
2wetFADTryptophan 5-halogenase/0.446
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.446
3m12FADMonomeric sarcosine oxidase1.5.3.10.446
4aosFADSteroid monooxygenase/0.446
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.446
4kwhNAPReductase homolog/0.446
4rv9SAHD-mycarose 3-C-methyltransferase/0.446
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.445
1f0xFADD-lactate dehydrogenase1.1.1.280.445
1hrvSDZGenome polyprotein/0.445
1ps9FAD2,4-dienoyl-CoA reductase1.3.1.340.445
1qf4RPDAdenylosuccinate synthetase/0.445
2cduFADNADH oxidase/0.445
2ekpNAD2-deoxy-D-gluconate 3-dehydrogenase/0.445
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.445
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.445
3qlrNDPDihydrofolate reductase1.5.1.30.445
4h4vFADBiphenyl dioxygenase ferredoxin reductase subunit/0.445
2i0zFADNAD(FAD)-utilizing dehydrogenases/0.444
2zb3NDPProstaglandin reductase 21.3.1.480.444
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.443
1kbjFMNCytochrome b2, mitochondrial1.1.2.30.443
1kt3RTLRetinol-binding protein 4/0.443
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.443
1xe55FEPlasmepsin-23.4.23.390.443
2vq7FADPutative flavin-containing monooxygenase/0.443
2vqbFADPutative flavin-containing monooxygenase/0.443
2y05NAPProstaglandin reductase 1/0.443
2y8qADP5'-AMP-activated protein kinase subunit gamma-1/0.443
3ka7FADPutative oxidoreductase/0.443
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.443
4mokFADPyranose 2-oxidase/0.443
4ytnFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.443
5i39FADL-amino acid deaminase/0.443
1e3wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.442
1gerFADGlutathione reductase1.8.1.70.442
1ha3MAUElongation factor Tu-A/0.442
2fjbSFDAdenylylsulfate reductase, subunit A (AprA)/0.442
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.442
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.442
4b67FADL-ornithine N(5)-monooxygenase/0.442
4rrwLURProstaglandin G/H synthase 21.14.99.10.442
4rrzLURProstaglandin G/H synthase 21.14.99.10.442
1f8wFADNADH peroxidase1.11.1.10.441
1gesFADGlutathione reductase1.8.1.70.441
1ja1NAPNADPH--cytochrome P450 reductase/0.441
1p7cT5AThymidine kinase/0.441
1xq6NAPUncharacterized protein At5g02240/0.441
4b5pACOAlpha-tubulin N-acetyltransferase 1/0.441
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4m9aFDAAcyl-CoA dehydrogenase/0.441
4nbuNAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.441
5jlaNADPutative short-chain dehydrogenase/reductase/0.441
1cg1IMOAdenylosuccinate synthetase/0.440
1diuBDMDihydrofolate reductase1.5.1.30.440
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.440
1iyzNDPProbable quinone oxidoreductase/0.440
1mo9FAD2-oxopropyl-CoM reductase, carboxylating1.8.1.50.440
1pqc444Oxysterols receptor LXR-beta/0.440
2dw4FADLysine-specific histone demethylase 1A10.440
2gv8FADThiol-specific monooxygenase1.14.130.440
2r26CMCCitrate synthase2.3.3.160.440
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.440
3orzBI43-phosphoinositide-dependent protein kinase 12.7.11.10.440
3s7a684Dihydrofolate reductase1.5.1.30.440
3vrtYS2Vitamin D3 receptor/0.440
3w8fNAD3-hydroxybutyrate dehydrogenase/0.440
4h4sFADBiphenyl dioxygenase ferredoxin reductase subunit/0.440
4hxyNDPPlm1/0.440
4l1xNAPAldo-keto reductase family 1 member C2/0.440
4rpgFADUDP-galactopyranose mutase5.4.99.90.440
4y9rNAPNADPH--cytochrome P450 reductase/0.440