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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
3opmLUIDipeptidyl peptidase 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3opmLUIDipeptidyl peptidase 4/1.000
3ccc7ACDipeptidyl peptidase 4/0.675
3g0bT22Dipeptidyl peptidase 4/0.642
4a5sN7FDipeptidyl peptidase 4/0.628
3g0dXIHDipeptidyl peptidase 4/0.619
3g0gRUMDipeptidyl peptidase 4/0.607
3qbjNXZDipeptidyl peptidase 4/0.601
4g1f0WGDipeptidyl peptidase 4/0.598
2aj8SC3Dipeptidyl peptidase 4/0.573
3f8sPF2Dipeptidyl peptidase 4/0.558
2rgu356Dipeptidyl peptidase 4/0.554
3vjkM51Dipeptidyl peptidase 4/0.537
2f3rG5PGuanylate kinase2.7.4.80.523
3ccbB2YDipeptidyl peptidase 4/0.518
3vjlW94Dipeptidyl peptidase 4/0.513
4ffw715Dipeptidyl peptidase 4/0.501
4rvgTYDD-mycarose 3-C-methyltransferase/0.485
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.484
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.484
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.480
1z44FMNNADPH dehydrogenase/0.478
2x96RX3Angiotensin-converting enzyme3.4.15.10.478
3aezGDPPantothenate kinase2.7.1.330.472
2g247IGRenin3.4.23.150.470
3tr05GPGuanylate kinase/0.470
4q0kGA3Phytohormone-binding protein/0.469
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.468
1z48FMNNADPH dehydrogenase/0.467
3intGDUUDP-galactopyranose mutase5.4.99.90.465
3ukfGDUUDP-galactopyranose mutase/0.464
3v0p4GWHisto-blood group ABO system transferase/0.464
3wqmB29Diterpene synthase3.1.7.80.464
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.464
5cflC2EStimulator of interferon genes protein/0.464
4lutDCSAlanine racemase/0.463
2xuoTZ4Acetylcholinesterase3.1.1.70.462
3hf3FMNChromate reductase/0.462
2pj4414Carboxypeptidase B/0.461
1h22E10Acetylcholinesterase3.1.1.70.460
2h8xFMNXenA/0.460
2oaeAILDipeptidyl peptidase 4/0.460
3l5lFMNXenobiotic reductase/0.460
4ca63EFAngiotensin-converting enzyme3.2.10.458
4loi1YCStimulator of interferon genes protein/0.458
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.458
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.457
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.457
2gesCOKPantothenate kinase2.7.1.330.457
2xugTZ4Acetylcholinesterase3.1.1.70.457
4awtFMNNADH:flavin oxidoreductase Sye1/0.457
4gdcNDPUDP-galactopyranose mutase/0.457
1jil485Tyrosine--tRNA ligase/0.456
1icsFMN12-oxophytodienoate reductase 11.3.1.420.455
1nhkCMPNucleoside diphosphate kinase2.7.4.60.455
4gddNAIUDP-galactopyranose mutase/0.455
3gf4UPGUDP-galactopyranose mutase5.4.99.90.454
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.453
2an9GDPGuanylate kinase2.7.4.80.453
2bf4FADNADPH--cytochrome P450 reductase/0.453
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.453
4b7zQ4QAcetylcholinesterase3.1.1.70.453
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.453
2x92X92Angiotensin-converting enzyme3.4.15.10.452
4f5yC2EStimulator of interferon genes protein/0.452
4nesUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.452
3in9H1SHeparin lyase I/0.451
3udj092Beta-secretase 13.4.23.460.451
3v0o4GWHisto-blood group ABO system transferase/0.451
4yxm2BADNA integrity scanning protein DisA/0.451
3apwDP0Alpha-1-acid glycoprotein 2/0.450
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.449
2g8yNADHydroxycarboxylate dehydrogenase B/0.449
2xpwOTCTetracycline repressor protein class D/0.449
3af0GDPPantothenate kinase2.7.1.330.449
3jszUPGUncharacterized protein/0.449
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.449
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.449
2zsaADPPantothenate kinase2.7.1.330.448
3ivmZPRProlyl endopeptidase/0.448
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.448
3qgf46FGenome polyprotein2.7.7.480.448
4dieC5PCytidylate kinase/0.448
4r81FMNPredicted NADH dehydrogenase/0.448
4rvfTYDD-mycarose 3-C-methyltransferase/0.448
1vftDCSAlanine racemase/0.447
2ifaFMNUncharacterized protein/0.447
2w6cBM4Acetylcholinesterase3.1.1.70.447
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4uthFMNXenobiotic reductase/0.447
3h2sNDPPutative NADH-flavin reductase/0.446
4e2yJHZMethyltransferase/0.446
1aa6MGDFormate dehydrogenase H1.1.99.330.445
1n2hPAJPantothenate synthetase6.3.2.10.445
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.445
3ziuLSSLeucyl-tRNA synthetase/0.445
4j7hTRHPCZA361.3/0.445
4xguADPPutative pachytene checkpoint protein 2/0.445
1ykiFMNOxygen-insensitive NAD(P)H nitroreductase/0.444
3d91REMRenin3.4.23.150.444
3ivxFG6Pantothenate synthetase6.3.2.10.444
4h12SAHHistone-lysine N-methyltransferase SETD22.1.1.430.444
4mvcCDCCholine-phosphate cytidylyltransferase A/0.444
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
3frkTQPQdtB/0.443
1h50FMNPentaerythritol tetranitrate reductase/0.442
1jcq739Protein farnesyltransferase subunit beta2.5.1.580.442
2gv8NDPThiol-specific monooxygenase1.14.130.442
2rlcCHDCholoylglycine hydrolase3.5.1.240.442
2x3jATPAcsD/0.442
3hdyGDUUDP-galactopyranose mutase/0.442
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.442
4nauAGSPhosphopantetheine adenylyltransferase/0.442
5cfpC2EStimulator of interferon genes protein/0.442
1w6hTITPlasmepsin-23.4.23.390.441
3lzxFADFerredoxin--NADP reductase 21.18.1.20.441
3muoZPRProlyl endopeptidase/0.441
4dya0MFNucleoprotein/0.441
5czySAMEukaryotic huntingtin interacting protein B/0.441
1odcA8BAcetylcholinesterase3.1.1.70.440
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.440
2cekN8TAcetylcholinesterase3.1.1.70.440
2geuCOKPantothenate kinase2.7.1.330.440
2gevCOKPantothenate kinase2.7.1.330.440
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.440
4flkY10Methionine aminopeptidase 1/0.440