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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
3vjkM51Dipeptidyl peptidase 4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3vjkM51Dipeptidyl peptidase 4/1.000
3vjlW94Dipeptidyl peptidase 4/0.779
3f8sPF2Dipeptidyl peptidase 4/0.630
3ccbB2YDipeptidyl peptidase 4/0.628
3qbjNXZDipeptidyl peptidase 4/0.622
4ffw715Dipeptidyl peptidase 4/0.573
3ccc7ACDipeptidyl peptidase 4/0.568
3opmLUIDipeptidyl peptidase 4/0.565
2rgu356Dipeptidyl peptidase 4/0.539
2aj8SC3Dipeptidyl peptidase 4/0.524
4g1f0WGDipeptidyl peptidase 4/0.515
2oaeAILDipeptidyl peptidase 4/0.497
1odcA8BAcetylcholinesterase3.1.1.70.490
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.484
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.484
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.483
2ckmAA7Acetylcholinesterase3.1.1.70.478
3hgoFMN12-oxophytodienoate reductase 31.3.1.420.473
3wqmB29Diterpene synthase3.1.7.80.472
4gdcNDPUDP-galactopyranose mutase/0.470
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3hdyGDUUDP-galactopyranose mutase/0.465
1ja1FMNNADPH--cytochrome P450 reductase/0.464
3g0cRUFDipeptidyl peptidase 4/0.464
2xuqTZ4Acetylcholinesterase3.1.1.70.462
2xukTZ5Acetylcholinesterase3.1.1.70.461
2xugTZ4Acetylcholinesterase3.1.1.70.460
3g0gRUMDipeptidyl peptidase 4/0.460
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.460
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.459
2cekN8TAcetylcholinesterase3.1.1.70.459
2whqHI6Acetylcholinesterase3.1.1.70.459
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.459
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.459
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.457
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.457
1vhzAPRADP compounds hydrolase NudE3.6.10.456
2xuoTZ4Acetylcholinesterase3.1.1.70.456
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3gf4UPGUDP-galactopyranose mutase5.4.99.90.455
4dyn0MRNucleoprotein/0.454
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.453
3ziuLSSLeucyl-tRNA synthetase/0.453
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.452
3tr05GPGuanylate kinase/0.452
4j4nD44Peptidylprolyl isomerase/0.452
1qpl587Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.450
3mj4URMUDP-galactopyranose mutase/0.450
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.449
4b64NAPL-ornithine N(5)-monooxygenase/0.449
1icpFMN12-oxophytodienoate reductase 11.3.1.420.448
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.448
1icqFMN12-oxophytodienoate reductase 11.3.1.420.447
1ja0FMNNADPH--cytochrome P450 reductase/0.447
1vfsDCSAlanine racemase/0.447
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3o5rFK5Peptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.447
4nv1TYDFormyl transferase/0.447
1kw0H4BPhenylalanine-4-hydroxylase1.14.16.10.446
1tllFMNNitric oxide synthase, brain1.14.13.390.446
2g247IGRenin3.4.23.150.446
2xufTZ4Acetylcholinesterase3.1.1.70.446
3pkdY10Methionine aminopeptidase 2/0.446
5ah5LSSLeucine--tRNA ligase/0.446
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.445
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.445
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.445
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.444
2geuCOKPantothenate kinase2.7.1.330.444
2qimZEAClass 10 plant pathogenesis-related protein/0.444
2zevIPEGeranylgeranyl pyrophosphate synthase/0.444
4h9tHL4Phosphotriesterase/0.444
1xvaSAMGlycine N-methyltransferase2.1.1.200.443
3pkaY02Methionine aminopeptidase 2/0.443
3ukfGDUUDP-galactopyranose mutase/0.443
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.442
4nv10FXFormyl transferase/0.442
1z6tADPApoptotic protease-activating factor 1/0.441
2cv2GSUGlutamate--tRNA ligase6.1.1.170.441
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.441
2gywOBIAcetylcholinesterase3.1.1.70.441
2xuhTZ4Acetylcholinesterase3.1.1.70.441
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.441
3pm1ETHTH-type transcriptional regulator QacR/0.441
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
1pqc444Oxysterols receptor LXR-beta/0.440
2abbFMNPentaerythritol tetranitrate reductase/0.440
2g1n1IGRenin3.4.23.150.440
2xupTZ5Acetylcholinesterase3.1.1.70.440
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.440