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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
2rgu356Dipeptidyl peptidase 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2rgu356Dipeptidyl peptidase 4/1.000
4g1f0WGDipeptidyl peptidase 4/0.654
3opmLUIDipeptidyl peptidase 4/0.627
3ccc7ACDipeptidyl peptidase 4/0.618
3g0gRUMDipeptidyl peptidase 4/0.589
3f8sPF2Dipeptidyl peptidase 4/0.584
3qbjNXZDipeptidyl peptidase 4/0.580
3vjkM51Dipeptidyl peptidase 4/0.578
3g0dXIHDipeptidyl peptidase 4/0.577
2aj8SC3Dipeptidyl peptidase 4/0.571
3g0bT22Dipeptidyl peptidase 4/0.570
4a5sN7FDipeptidyl peptidase 4/0.565
4ffw715Dipeptidyl peptidase 4/0.551
3vjlW94Dipeptidyl peptidase 4/0.531
3ccbB2YDipeptidyl peptidase 4/0.530
2oaeAILDipeptidyl peptidase 4/0.517
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.490
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.490
2xuoTZ4Acetylcholinesterase3.1.1.70.482
4araC56Acetylcholinesterase3.1.1.70.475
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.470
1h22E10Acetylcholinesterase3.1.1.70.467
1icsFMN12-oxophytodienoate reductase 11.3.1.420.467
2qimZEAClass 10 plant pathogenesis-related protein/0.465
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.464
3q43D66M1 family aminopeptidase3.4.110.463
3wqmB29Diterpene synthase3.1.7.80.463
4ey7E20Acetylcholinesterase3.1.1.70.462
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.462
2xupTZ5Acetylcholinesterase3.1.1.70.461
3h3r14HCollagen type IV alpha-3-binding protein/0.461
1nhkCMPNucleoside diphosphate kinase2.7.4.60.460
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.460
1icpFMN12-oxophytodienoate reductase 11.3.1.420.459
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2dxdANPNucleoside diphosphate kinase2.7.4.60.459
4awsFMNNADH:flavin oxidoreductase Sye1/0.459
4dya0MFNucleoprotein/0.459
2iyfERYOleandomycin glycosyltransferase2.4.10.458
4b63NAPL-ornithine N(5)-monooxygenase/0.458
1icqFMN12-oxophytodienoate reductase 11.3.1.420.457
4d2dALA_ALA_ALADi-or tripeptide:H+ symporter/0.457
2xuiTZ5Acetylcholinesterase3.1.1.70.456
3hl0NADMaleylacetate reductase/0.456
3k1wBFXRenin3.4.23.150.456
4lh71X8DNA ligase/0.456
3h3qH13Collagen type IV alpha-3-binding protein/0.455
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.453
2xq0BESLeukotriene A-4 hydrolase homolog3.3.2.60.453
1odcA8BAcetylcholinesterase3.1.1.70.452
2whqHI6Acetylcholinesterase3.1.1.70.452
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.452
2cekN8TAcetylcholinesterase3.1.1.70.451
2xufTZ4Acetylcholinesterase3.1.1.70.451
3v2uATPProtein GAL3/0.451
1xvaSAMGlycine N-methyltransferase2.1.1.200.449
2j3qTFLAcetylcholinesterase3.1.1.70.449
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
3c8bARG_ARG_GLY_ILE_NH2Botulinum neurotoxin type A3.4.24.690.448
3ftxBESLeukotriene A-4 hydrolase3.3.2.60.448
3hdyGDUUDP-galactopyranose mutase/0.448
4bzbDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.448
4zgsNADPutative D-lactate dehydrogenase/0.448
3oadLPORenin3.4.23.150.447
3ukfGDUUDP-galactopyranose mutase/0.447
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.447
1jcq739Protein farnesyltransferase subunit beta2.5.1.580.446
2g247IGRenin3.4.23.150.446
2h8xFMNXenA/0.446
1ffyMRCIsoleucine--tRNA ligase6.1.1.50.445
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.445
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.445
2yd0BESEndoplasmic reticulum aminopeptidase 13.4.110.445
4j4nD44Peptidylprolyl isomerase/0.445
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.444
1x8lOXRRetinol dehydratase/0.444
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.444
2il2LIXRenin3.4.23.150.444
3kybFMNUDP-galactopyranose mutase5.4.99.90.444
3v0p4GWHisto-blood group ABO system transferase/0.444
2ea4F79Methionine aminopeptidase 2/0.443
3zkiWZVBeta-secretase 23.4.23.450.443
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.442
1q84TZ4Acetylcholinesterase3.1.1.70.442
2x96RX3Angiotensin-converting enzyme3.4.15.10.442
2xugTZ4Acetylcholinesterase3.1.1.70.442
4b7zQ4QAcetylcholinesterase3.1.1.70.442
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.442
5kwvANPPantothenate synthetase/0.442
2q92B23Methionine aminopeptidase/0.441
2r8pT6FTransketolase 1/0.441
3hdqGDUUDP-galactopyranose mutase/0.441
3tr05GPGuanylate kinase/0.441
1qpl587Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
3q7fED2Uncharacterized protein/0.440
3vaxPLPUncharacterized protein/0.440