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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
3g0bT22Dipeptidyl peptidase 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3g0bT22Dipeptidyl peptidase 4/1.000
3g0dXIHDipeptidyl peptidase 4/0.728
3g0gRUMDipeptidyl peptidase 4/0.725
3ccc7ACDipeptidyl peptidase 4/0.669
3opmLUIDipeptidyl peptidase 4/0.639
4a5sN7FDipeptidyl peptidase 4/0.604
4g1f0WGDipeptidyl peptidase 4/0.570
3qbjNXZDipeptidyl peptidase 4/0.549
2aj8SC3Dipeptidyl peptidase 4/0.546
3g0cRUFDipeptidyl peptidase 4/0.538
3f8sPF2Dipeptidyl peptidase 4/0.515
4rvgTYDD-mycarose 3-C-methyltransferase/0.514
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.506
3v0p4GWHisto-blood group ABO system transferase/0.499
2f3rG5PGuanylate kinase2.7.4.80.496
2gesCOKPantothenate kinase2.7.1.330.495
2rlcCHDCholoylglycine hydrolase3.5.1.240.488
5kwvANPPantothenate synthetase/0.488
3tr05GPGuanylate kinase/0.486
4ffw715Dipeptidyl peptidase 4/0.486
2xuoTZ4Acetylcholinesterase3.1.1.70.484
4j4nD44Peptidylprolyl isomerase/0.483
2rgu356Dipeptidyl peptidase 4/0.482
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.481
3af1GDPPantothenate kinase2.7.1.330.480
1h22E10Acetylcholinesterase3.1.1.70.479
4j0v1H7Beta-secretase 13.4.23.460.479
3wqmB29Diterpene synthase3.1.7.80.478
4f5yC2EStimulator of interferon genes protein/0.478
2zsaADPPantothenate kinase2.7.1.330.477
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.477
2g247IGRenin3.4.23.150.476
3d91REMRenin3.4.23.150.476
3gf4UPGUDP-galactopyranose mutase5.4.99.90.476
4gdcNDPUDP-galactopyranose mutase/0.476
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.476
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.475
4rvfTYDD-mycarose 3-C-methyltransferase/0.475
1r6tTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.474
2geuCOKPantothenate kinase2.7.1.330.474
2ixkTDOdTDP-4-dehydrorhamnose 3,5-epimerase5.1.3.130.474
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.473
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.473
3lqfNADGalactitol dehydrogenase/0.471
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.470
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.470
4q0kGA3Phytohormone-binding protein/0.470
1w6hTITPlasmepsin-23.4.23.390.469
1z44FMNNADPH dehydrogenase/0.469
2zueANPArginine--tRNA ligase6.1.1.190.469
3mj4URMUDP-galactopyranose mutase/0.469
3vjlW94Dipeptidyl peptidase 4/0.469
1q84TZ4Acetylcholinesterase3.1.1.70.468
2xpwOTCTetracycline repressor protein class D/0.468
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.468
4gddNAIUDP-galactopyranose mutase/0.468
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.468
4lcjNADC-terminal-binding protein 2/0.468
2x92X92Angiotensin-converting enzyme3.4.15.10.467
2x95X95Angiotensin-converting enzyme3.4.15.10.467
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.467
2iko7IGRenin3.4.23.150.466
2xy3DUPSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.466
3k5c0BIBeta-secretase 13.4.23.460.466
4lutDCSAlanine racemase/0.466
3ihkTPPUncharacterized protein/0.465
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.465
3in9H1SHeparin lyase I/0.464
3rsv3RSBeta-secretase 13.4.23.460.464
4bxk1IUAngiotensin-converting enzyme3.2.10.464
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.464
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.464
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.464
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.464
2x96RX3Angiotensin-converting enzyme3.4.15.10.463
2yd0BESEndoplasmic reticulum aminopeptidase 13.4.110.463
3l67FMNXenobiotic reductase/0.463
2b58COADiamine acetyltransferase 1/0.462
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.461
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.461
3tjzGNPADP-ribosylation factor 1/0.461
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.461
4nesUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.461
1o1s1NHProtein farnesyltransferase subunit beta2.5.1.580.460
2cekN8TAcetylcholinesterase3.1.1.70.460
2g1s4IGRenin3.4.23.150.460
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.460
4b63NAPL-ornithine N(5)-monooxygenase/0.460
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.460
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.460
4twrNADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase/0.460
5cfpC2EStimulator of interferon genes protein/0.460
5czySAMEukaryotic huntingtin interacting protein B/0.460
1odcA8BAcetylcholinesterase3.1.1.70.459
2c20NADUDP-glucose 4-epimerase/0.459
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.459
3ccbB2YDipeptidyl peptidase 4/0.459
3junAJDPhenazine biosynthesis protein A/B/0.459
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.459
4awtFMNNADH:flavin oxidoreductase Sye1/0.459
4ewo996Beta-secretase 13.4.23.460.459
4j0t6T9Beta-secretase 13.4.23.460.459
4m83ERYOleandomycin glycosyltransferase2.4.10.459
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.458
2xlrFADPutative flavin-containing monooxygenase/0.458
2xugTZ4Acetylcholinesterase3.1.1.70.458
2bf4FADNADPH--cytochrome P450 reductase/0.457
2ha6SCKAcetylcholinesterase3.1.1.70.457
2ikuLIYRenin3.4.23.150.457
2pj4414Carboxypeptidase B/0.457
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.457
1rfuADPPyridoxal kinase2.7.1.350.456
2x97RX4Angiotensin-converting enzyme3.4.15.10.456
3zhsTD6Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.456
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.456
4xguADPPutative pachytene checkpoint protein 2/0.456
5c3aURMHisto-blood group ABO system transferase/0.456
2g226IGRenin3.4.23.150.455
2il2LIXRenin3.4.23.150.455
2trtTACTetracycline repressor protein class D/0.455
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.455
4yxm2BADNA integrity scanning protein DisA/0.455
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.454
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.454
4jayNAPUDP-N-acetylenolpyruvoylglucosamine reductase/0.454
4uugPXGBranched-chain amino acid aminotransferase, putative/0.454
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.453
1xe65FPPlasmepsin-23.4.23.390.453
2g1y5IGRenin3.4.23.150.453
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.453
3c8aARG_ARG_GLY_LEU_NH2Botulinum neurotoxin type A3.4.24.690.453
4araC56Acetylcholinesterase3.1.1.70.453
2gevCOKPantothenate kinase2.7.1.330.452
2gv8NDPThiol-specific monooxygenase1.14.130.452
2i4qUA4Renin3.4.23.150.452
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.452
2w6cBM4Acetylcholinesterase3.1.1.70.452
2whqHI6Acetylcholinesterase3.1.1.70.452
2xlpFADPutative flavin-containing monooxygenase/0.452
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.452
2oapANPType II secretion system protein (GspE-2)/0.451
3h0bB35Beta-secretase 13.4.23.460.451
3lqsPSZD-alanine aminotransferase2.6.1.210.451
3melTPPThiamin pyrophosphokinase family protein/0.451
4e2yJHZMethyltransferase/0.451
4ey7E20Acetylcholinesterase3.1.1.70.451
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.451
4kgkGTPUncharacterized protein/0.451
1q83TZ5Acetylcholinesterase3.1.1.70.450
2ifaFMNUncharacterized protein/0.450
3qdlFMNOxygen-insensitive NADPH nitroreductase/0.450
4g67SAHUncharacterized ACR, COG1565 superfamily/0.450
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.450
1f8wFADNADH peroxidase1.11.1.10.449
1yidATPTryptophan--tRNA ligase 26.1.1.20.449
2futH1SHeparin and heparin-sulfate lyase/0.449
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.449
3kej3EJCollagenase 33.4.240.449
3nsh957Beta-secretase 13.4.23.460.449
3r95ACOMccE protein/0.449
3zkiWZVBeta-secretase 23.4.23.450.449
4i0i957Beta-secretase 13.4.23.460.449
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.448
1z41FMNNADPH dehydrogenase/0.448
3ag6PAJPantothenate synthetase/0.448
3ekuCY9Actin-5C/0.448
3l5lFMNXenobiotic reductase/0.448
4exg916Beta-secretase 13.4.23.460.448
5jqhCAUBeta-2 adrenergic receptor/0.448
1ja1FMNNADPH--cytochrome P450 reductase/0.447
1ld7U66Protein farnesyltransferase subunit beta2.5.1.580.447
1tiqCOASpermidine/spermine N(1)-acetyltransferase/0.447
1xvaSAMGlycine N-methyltransferase2.1.1.200.447
2ckmAA7Acetylcholinesterase3.1.1.70.447
2oz57XYUncharacterized protein/0.447
2xupTZ5Acetylcholinesterase3.1.1.70.447
3af4GCPPantothenate kinase2.7.1.330.447
3d3xARG_ILE_MET_GLU_NH2Type E botulinum toxin/0.447
3f1kNAPUncharacterized oxidoreductase YciK10.447
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.447
3fktSIIBeta-secretase 13.4.23.460.447
4hdgGTPGenome polyprotein2.7.7.480.447
1jil485Tyrosine--tRNA ligase/0.446
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.446
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.446
2b3vACODiamine acetyltransferase 1/0.446
2x90EALAngiotensin-converting enzyme3.4.15.10.446
3b70NAPEnoyl reductase LovC10.446
3pkdY10Methionine aminopeptidase 2/0.446
3q7fED2Uncharacterized protein/0.446
3vydVYDRenin3.4.23.150.446
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.446
1eveE20Acetylcholinesterase3.1.1.70.445
1joaFADNADH peroxidase1.11.1.10.445
1obbNADAlpha-glucosidase3.2.1.200.445
1tehNADAlcohol dehydrogenase class-31.1.1.10.445
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.445
2g1r3IGRenin3.4.23.150.445
2hizLIJBeta-secretase 13.4.23.460.445
3af0GDPPantothenate kinase2.7.1.330.445
3hl0NADMaleylacetate reductase/0.445
3ukfGDUUDP-galactopyranose mutase/0.445
3vyfVYFRenin3.4.23.150.445
4azy7F3Beta-secretase 13.4.23.460.445
4fkzUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.445
5dldUD1UDP-N-Acetylglucosamine 2-epimerase/0.445
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.444
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.444
2x3fAPCPantothenate synthetase/0.444
2z9dFMNFMN-dependent NADH-azoreductase/0.444
3c8bARG_ARG_GLY_ILE_NH2Botulinum neurotoxin type A3.4.24.690.444
3intGDUUDP-galactopyranose mutase5.4.99.90.444
3muoZPRProlyl endopeptidase/0.444
3sfy3FYUncharacterized protein/0.444
3ziuLSSLeucyl-tRNA synthetase/0.444
4bftZVTPantothenate kinase2.7.1.330.444
4ycpFMNtRNA-dihydrouridine(16) synthase/0.444
1bduDURThymidylate synthase/0.443
1h73ANPHomoserine kinase2.7.1.390.443
1vftDCSAlanine racemase/0.443
1xe55FEPlasmepsin-23.4.23.390.443
3aho3A2Oligopeptidase/0.443
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.443
4ca63EFAngiotensin-converting enzyme3.2.10.443
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.443
4tlzNAPKtzI/0.443
1j36LPRAngiotensin-converting enzyme3.4.15.10.442
1n7hNDPGDP-mannose 4,6 dehydratase 24.2.1.470.442
1psa0ZLPepsin A3.4.23.10.442
1reqDCAMethylmalonyl-CoA mutase large subunit5.4.99.20.442
1udbUFGUDP-glucose 4-epimerase5.1.3.20.442
1xjqADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.442
1yqdNAPSinapyl alcohol dehydrogenase/0.442
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.442
2qjoNADBifunctional NMN adenylyltransferase/Nudix hydrolase2.7.7.10.442
2xefAR8Glutamate carboxypeptidase 23.4.17.210.442
3mauEXTPutative sphingosine-1-phosphate lyase/0.442
3q9bB3NAcetylpolyamine amidohydrolase/0.442
4ambDUDPutative glycosyl transferase/0.442
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.442
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.442
1bim0QBRenin3.4.23.150.441
1rneC60Renin3.4.23.150.441
2eixFADNADH-cytochrome b5 reductase/0.441
2vn1FK5Peptidylprolyl isomerase/0.441
3cosNADAlcohol dehydrogenase 41.1.1.10.441
3enkUPGUDP-glucose 4-epimerase/0.441
3fccATPD-alanine--poly(phosphoribitol) ligase subunit 1/0.441
3gqvNAPEnoyl reductase LovC10.441
3hyoADPPyridoxal kinase/0.441
4a87NARMajor pollen allergen Bet v 1-A/0.441
4frkDWDBeta-secretase 13.4.23.460.441
4fue7UPUrokinase-type plasminogen activator3.4.21.730.441
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
1kbiFMNCytochrome b2, mitochondrial1.1.2.30.440
1xdpATPPolyphosphate kinase/0.440
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.440
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.440
3b1dPLSBetaC-S lyase/0.440
3qgf46FGenome polyprotein2.7.7.480.440
4h12SAHHistone-lysine N-methyltransferase SETD22.1.1.430.440
4hmvWUBPhenazine biosynthesis protein PhzG1.40.440
4opgFDAConserved Archaeal protein/0.440