Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3opmLUIDipeptidyl peptidase 4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3opmLUIDipeptidyl peptidase 4/1.000
3ccc7ACDipeptidyl peptidase 4/0.674
3g0bT22Dipeptidyl peptidase 4/0.652
4a5sN7FDipeptidyl peptidase 4/0.627
4g1f0WGDipeptidyl peptidase 4/0.622
3g0dXIHDipeptidyl peptidase 4/0.619
3g0gRUMDipeptidyl peptidase 4/0.611
3qbjNXZDipeptidyl peptidase 4/0.601
2aj8SC3Dipeptidyl peptidase 4/0.573
3f8sPF2Dipeptidyl peptidase 4/0.558
2rgu356Dipeptidyl peptidase 4/0.552
2f3rG5PGuanylate kinase2.7.4.80.517
3vjlW94Dipeptidyl peptidase 4/0.513
4ffw715Dipeptidyl peptidase 4/0.501
1z44FMNNADPH dehydrogenase/0.486
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.485
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.485
1icpFMN12-oxophytodienoate reductase 11.3.1.420.484
3muoZPRProlyl endopeptidase/0.480
2zsaADPPantothenate kinase2.7.1.330.477
4gdcNDPUDP-galactopyranose mutase/0.476
4lutDCSAlanine racemase/0.474
3tr05GPGuanylate kinase/0.472
4q0kGA3Phytohormone-binding protein/0.466
2whqHI6Acetylcholinesterase3.1.1.70.465
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.465
2a5hSAML-lysine 2,3-aminomutase5.4.3.20.463
3wqmB29Diterpene synthase3.1.7.80.463
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.462
1z41FMNNADPH dehydrogenase/0.462
2h8xFMNXenA/0.461
2hfuMEVMevalonate kinase/0.461
2xuoTZ4Acetylcholinesterase3.1.1.70.461
3to3ATPPetrobactin biosynthesis protein AsbB/0.461
3v0p4GWHisto-blood group ABO system transferase/0.461
1h22E10Acetylcholinesterase3.1.1.70.460
4rvgTYDD-mycarose 3-C-methyltransferase/0.460
2oaeAILDipeptidyl peptidase 4/0.459
3ivmZPRProlyl endopeptidase/0.458
2gesCOKPantothenate kinase2.7.1.330.457
2xugTZ4Acetylcholinesterase3.1.1.70.457
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.457
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.457
4f5yC2EStimulator of interferon genes protein/0.456
3aezGDPPantothenate kinase2.7.1.330.455
3ukfGDUUDP-galactopyranose mutase/0.455
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.455
1p4aPCPPur operon repressor/0.454
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.454
3intGDUUDP-galactopyranose mutase5.4.99.90.454
1z48FMNNADPH dehydrogenase/0.453
1jil485Tyrosine--tRNA ligase/0.452
1w6rGNTAcetylcholinesterase3.1.1.70.452
2g247IGRenin3.4.23.150.452
3ksqZ96Protein farnesyltransferase subunit beta2.5.1.580.452
3l5lFMNXenobiotic reductase/0.452
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.452
1bwlFMNNADPH dehydrogenase 11.6.99.10.451
3kt3TYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.451
4b7zQ4QAcetylcholinesterase3.1.1.70.451
4c49HCYCorticosteroid-binding globulin/0.451
2zsbADPPantothenate kinase2.7.1.330.450
3h0bB35Beta-secretase 13.4.23.460.450
3hf3FMNChromate reductase/0.450
4loi1YCStimulator of interferon genes protein/0.450
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
1x1cSAHC-20 methyltransferase/0.449
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.449
3apwDP0Alpha-1-acid glycoprotein 2/0.449
3fvlBHKCarboxypeptidase A13.4.17.10.449
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.449
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.449
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.449
4r81FMNPredicted NADH dehydrogenase/0.449
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.448
1wkhPPE[LysW]-aminoadipate semialdehyde transaminase/0.448
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.448
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.448
5c3aURMHisto-blood group ABO system transferase/0.448
1szgFNSCytochrome b2, mitochondrial1.1.2.30.447
2ex1C5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.447
4awtFMNNADH:flavin oxidoreductase Sye1/0.447
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.447
5cflC2EStimulator of interferon genes protein/0.447
1n2iPAJPantothenate synthetase6.3.2.10.446
2an9GDPGuanylate kinase2.7.4.80.446
2w6cBM4Acetylcholinesterase3.1.1.70.446
3qgf46FGenome polyprotein2.7.7.480.446
3v0o4GWHisto-blood group ABO system transferase/0.446
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.445
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3ziuLSSLeucyl-tRNA synthetase/0.445
4gddNAIUDP-galactopyranose mutase/0.445
4j7hTRHPCZA361.3/0.445
4mvcCDCCholine-phosphate cytidylyltransferase A/0.445
5ah5LSSLeucine--tRNA ligase/0.445
5czySAMEukaryotic huntingtin interacting protein B/0.445
1dx6GNTAcetylcholinesterase3.1.1.70.444
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.444
3frkTQPQdtB/0.444
4d6qPD2Lysine-specific demethylase 4D1.14.110.444
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.444
1nhkCMPNucleoside diphosphate kinase2.7.4.60.443
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.443
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.443
1vftDCSAlanine racemase/0.443
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
3h2sNDPPutative NADH-flavin reductase/0.443
3hdyGDUUDP-galactopyranose mutase/0.443
3udj092Beta-secretase 13.4.23.460.443
1h50FMNPentaerythritol tetranitrate reductase/0.442
1jcq739Protein farnesyltransferase subunit beta2.5.1.580.442
2anb5GPGuanylate kinase2.7.4.80.442
3f1kNAPUncharacterized oxidoreductase YciK10.442
3jszUPGUncharacterized protein/0.442
4dieC5PCytidylate kinase/0.442
4gv8DUPDUTPase/0.442
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.442
4rvdSAMD-mycarose 3-C-methyltransferase/0.442
4wdgA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.441
4kc2WS2Histo-blood group ABO system transferase/0.441
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.440
1hb1OCVIsopenicillin N synthase1.21.3.10.440
1n2jPAFPantothenate synthetase6.3.2.10.440
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
3fvuIACKynurenine--oxoglutarate transaminase 12.6.1.70.440
4gtv7TRGeranylgeranyl transferase type-2 subunit beta2.5.1.600.440