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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
4bcdTDVProlyl endopeptidase3.4.21.26

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4bcdTDVProlyl endopeptidase3.4.21.261.000
1e8mP0HProlyl endopeptidase3.4.21.260.868
1uopGLY_PHE_GLU_PROProlyl endopeptidase3.4.21.260.699
3eq9X97Prolyl endopeptidase3.4.21.260.641
1uoqGLU_PHE_SER_PROProlyl endopeptidase3.4.21.260.639
1uooGLY_PHE_ARG_PROProlyl endopeptidase3.4.21.260.573
3hyoADPPyridoxal kinase/0.485
2pobGW4Peroxisome proliferator-activated receptor gamma/0.483
1cscCMCCitrate synthase, mitochondrial2.3.3.10.473
4fj1NAP17beta-hydroxysteroid dehydrogenase/0.472
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.471
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.470
4xw4ANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.470
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.469
4fj2NAP17beta-hydroxysteroid dehydrogenase/0.469
4f9mFCMPeroxisome proliferator-activated receptor gamma/0.468
2pg0FADAcyl-CoA dehydrogenase/0.467
2po7CHDFerrochelatase, mitochondrial4.99.1.10.467
4p5aFADFlavin-dependent thymidylate synthase/0.467
1kkq471Peroxisome proliferator-activated receptor alpha/0.463
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.462
2x92X92Angiotensin-converting enzyme3.4.15.10.461
3mx2TTPNucleoprotein/0.461
3s5wFADL-ornithine N(5)-monooxygenase/0.461
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.460
2eixFADNADH-cytochrome b5 reductase/0.460
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.459
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.458
1rdt570Peroxisome proliferator-activated receptor gamma/0.457
3wqmB29Diterpene synthase3.1.7.80.456
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
3fktSIIBeta-secretase 13.4.23.460.455
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.454
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.453
3toxNAPPutative oxidoreductase/0.453
3tqcADPPantothenate kinase/0.453
3udn09BBeta-secretase 13.4.23.460.453
4j0v1H7Beta-secretase 13.4.23.460.453
1icqOPD12-oxophytodienoate reductase 11.3.1.420.452
2ctsCOACitrate synthase, mitochondrial2.3.3.10.452
4xzjNADPutative NAD(+)--arginine ADP-ribosyltransferase Vis2.4.2.310.452
1pmn984Mitogen-activated protein kinase 102.7.11.240.451
2iviACWIsopenicillin N synthase1.21.3.10.451
4o8fBRLPeroxisome proliferator-activated receptor gamma/0.451
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.450
2wksCB63-dehydroquinate dehydratase4.2.1.100.450
2znnS44Peroxisome proliferator-activated receptor alpha/0.450
3cscACOCitrate synthase, mitochondrial2.3.3.10.450
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.450
2yxuATPPyridoxal kinase2.7.1.350.449
3qwfNAP17beta-hydroxysteroid dehydrogenase/0.449
4u2sFDACholesterol oxidase1.1.3.60.449
5burATP2-succinylbenzoate--CoA ligase/0.449
5irnADPNucleotide binding oligomerization domain containing 2/0.449
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.448
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.448
4jldADPAdenylate kinase/0.448
4jtqNAPAldo-keto reductase family 1 member C2/0.448
4wriOKAOkadaic acid binding protein 2-alpha/0.448
5hsaFASAlcohol oxidase 11.1.3.130.448
1ppjANYCytochrome b/0.447
2b3dFADModulator of drug activity B/0.447
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.447
2xb5I7TTetracycline repressor protein class D/0.447
3bgxMEFThymidylate synthase/0.447
3d91REMRenin3.4.23.150.447
3h2sNDPPutative NADH-flavin reductase/0.447
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
1yidATPTryptophan--tRNA ligase 26.1.1.20.446
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.446
3b1dPLSBetaC-S lyase/0.446
3gw9VNILanosterol 14-alpha-demethylase/0.446
3he3FADUDP-galactopyranose mutase/0.446
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.446
2ou2ACOHistone acetyltransferase KAT5/0.445
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.445
3qdlFMNOxygen-insensitive NADPH nitroreductase/0.445
3r7kFDAProbable acyl CoA dehydrogenase/0.445
4i0h1BLBeta-secretase 13.4.23.460.445
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.444
2eerNADNAD-dependent alcohol dehydrogenase1.1.1.10.444
3eq7X99Prolyl endopeptidase3.4.21.260.444
3fql79ZGenome polyprotein2.7.7.480.444
3v9y24LPeroxisome proliferator-activated receptor gamma/0.444
4bjzFADProbable salicylate monooxygenase/0.444
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.444
1njbUMPThymidylate synthase/0.443
2a4nCOAAac(6')-Ii protein/0.443
2q8sL92Peroxisome proliferator-activated receptor gamma/0.443
2trtTACTetracycline repressor protein class D/0.443
3b20NADGlyceraldehyde-3-phosphate dehydrogenase/0.443
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.443
3ohh3HHBeta-secretase 13.4.23.460.443
3q8uADPNucleoside diphosphate kinase/0.443
1fm4DXCMajor pollen allergen Bet v 1-L/0.442
1zptFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.442
3i0pNADMalate dehydrogenase, putative/0.442
3r3sNADPutative oxidoreductase/0.442
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.442
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.441
1xg5NAPDehydrogenase/reductase SDR family member 11/0.441
2b8l5HABeta-secretase 13.4.23.460.441
4frjDWBBeta-secretase 13.4.23.460.441
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
4p2lFADSulfhydryl oxidase 11.8.3.20.441
1h6dNDPGlucose--fructose oxidoreductase1.1.99.280.440
1jtuLYBThymidylate synthase/0.440
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.440
2npaMMBPeroxisome proliferator-activated receptor alpha/0.440
3lpiZ74Beta-secretase 13.4.23.460.440
4b63FADL-ornithine N(5)-monooxygenase/0.440
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.440
4frkDWDBeta-secretase 13.4.23.460.440
4jjiNADAlcohol dehydrogenase class-3/0.440