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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
3f8sPF2Dipeptidyl peptidase 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3f8sPF2Dipeptidyl peptidase 4/1.000
3vjkM51Dipeptidyl peptidase 4/0.614
3vjlW94Dipeptidyl peptidase 4/0.614
3qbjNXZDipeptidyl peptidase 4/0.594
3opmLUIDipeptidyl peptidase 4/0.549
3ccbB2YDipeptidyl peptidase 4/0.543
4ffw715Dipeptidyl peptidase 4/0.543
4g1f0WGDipeptidyl peptidase 4/0.536
3ccc7ACDipeptidyl peptidase 4/0.533
3g0bT22Dipeptidyl peptidase 4/0.527
2rgu356Dipeptidyl peptidase 4/0.524
2aj8SC3Dipeptidyl peptidase 4/0.499
3g0gRUMDipeptidyl peptidase 4/0.494
3g0dXIHDipeptidyl peptidase 4/0.486
2xuoTZ4Acetylcholinesterase3.1.1.70.471
2xugTZ4Acetylcholinesterase3.1.1.70.468
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.468
3dzkNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.464
2oaeAILDipeptidyl peptidase 4/0.462
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.461
4awsFMNNADH:flavin oxidoreductase Sye1/0.461
2a3bCFFEndochitinase B13.2.1.140.460
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.460
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.457
4arbC57Acetylcholinesterase3.1.1.70.455
4qg1DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.455
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.454
3rsv3RSBeta-secretase 13.4.23.460.453
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.452
4bfvZVVPantothenate kinase2.7.1.330.452
2xuqTZ4Acetylcholinesterase3.1.1.70.451
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.450
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.450
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.449
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.449
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.449
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.449
4gdcNDPUDP-galactopyranose mutase/0.449
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.449
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.448
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.448
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
2wzySQXSoluble acetylcholine receptor/0.447
3wqmB29Diterpene synthase3.1.7.80.447
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.447
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.446
4j4nD44Peptidylprolyl isomerase/0.445
2xufTZ4Acetylcholinesterase3.1.1.70.444
4j7hTRHPCZA361.3/0.444
3oe9ITDC-X-C chemokine receptor type 4/0.444
1q84TZ4Acetylcholinesterase3.1.1.70.443
2cv2GSUGlutamate--tRNA ligase6.1.1.170.443
2q92B23Methionine aminopeptidase/0.443
3h3t16HCollagen type IV alpha-3-binding protein/0.443
4drhRAPSerine/threonine-protein kinase mTOR2.7.11.10.443
4drhRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.443
4qfzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.443
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.442
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.442
3oduITDC-X-C chemokine receptor type 4/0.442
2gouFMNNADH:flavin oxidoreductase Sye1/0.441
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.440
3c1oNAPEugenol synthase/0.440
3hdyGDUUDP-galactopyranose mutase/0.440