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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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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
2hutSAHDiphthine synthase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2hutSAHDiphthine synthase/1.000
2owkSAHDiphthine synthase/0.836
2eh2SAHDiphthine synthase/0.832
2ek3SAHDiphthine synthase/0.828
2dv5SAHDiphthine synthase/0.789
2e15SAHDiphthine synthase/0.783
2ehlSAHDiphthine synthase/0.773
2p5fSAHDiphthine synthase/0.761
2ed5SAHDiphthine synthase/0.758
2ek2SAHDiphthine synthase/0.754
2e8rSAHDiphthine synthase/0.753
2e17SAHDiphthine synthase/0.749
2owgSAHDiphthine synthase/0.749
2p5cSAHDiphthine synthase/0.748
2dsiSAHDiphthine synthase/0.741
2z6rSAHDiphthine synthase/0.737
2emuSAHDiphthine synthase/0.736
2owuSAHDiphthine synthase/0.731
2p6iSAHDiphthine synthase/0.724
2dv7SAHDiphthine synthase/0.720
2eh5SAHDiphthine synthase/0.717
2eleSAHDiphthine synthase/0.714
2huvSAHDiphthine synthase/0.713
2p9dSAHDiphthine synthase/0.710
2dxxSAHDiphthine synthase/0.704
2huqSAHDiphthine synthase/0.704
2e4nSAHDiphthine synthase/0.694
2egsSAHDiphthine synthase/0.693
2pb5SAHDiphthine synthase/0.693
2p2xSAHDiphthine synthase/0.690
2ejkSAHDiphthine synthase/0.689
2eniSAHDiphthine synthase/0.689
2el0SAHDiphthine synthase/0.684
2el3SAHDiphthine synthase/0.684
2emrSAHDiphthine synthase/0.684
2pb6SAHDiphthine synthase/0.677
2e7rSAHDiphthine synthase/0.675
2eeqSAHDiphthine synthase/0.675
2p6dSAHDiphthine synthase/0.675
2dsgSAHDiphthine synthase/0.669
2hr8SAHDiphthine synthase/0.668
2dxwSAHDiphthine synthase/0.663
1wngSAHDiphthine synthase/0.662
2pcaSAHDiphthine synthase/0.662
2eldSAHDiphthine synthase/0.659
2p6kSAHDiphthine synthase/0.659
2pckSAHDiphthine synthase/0.658
2eh4SAHDiphthine synthase/0.655
2dxvSAHDiphthine synthase/0.652
2e8hSAHDiphthine synthase/0.652
2ek4SAHDiphthine synthase/0.644
2pcmSAHDiphthine synthase/0.643
1vceSAHDiphthine synthase/0.642
2pcgSAHDiphthine synthase/0.642
2e07SAHDiphthine synthase/0.640
2dv4SAHDiphthine synthase/0.639
2dekSAHDiphthine synthase/0.635
2ekaSAHDiphthine synthase/0.620
2dshSAHDiphthine synthase/0.614
2e8sSAHDiphthine synthase/0.609
2pciSAHDiphthine synthase/0.608
2dv3SAHDiphthine synthase/0.604
2ejjSAHDiphthine synthase/0.604
2e08SAHDiphthine synthase/0.603
2huxSAHDiphthine synthase/0.601
2owfSAHDiphthine synthase/0.601
2pchSAHDiphthine synthase/0.596
2p6lSAHDiphthine synthase/0.592
2egbSAHDiphthine synthase/0.591
2e8qSAHDiphthine synthase/0.588
2eglSAHDiphthine synthase/0.581
2pb4SAHDiphthine synthase/0.579
2ek7SAHDiphthine synthase/0.573
2e16SAHDiphthine synthase/0.570
2en5SAHDiphthine synthase/0.559
2owvSAHDiphthine synthase/0.556
2ed3SAHDiphthine synthase/0.551
2ejzSAHDiphthine synthase/0.529
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.471
1w6hTITPlasmepsin-23.4.23.390.468
4q71FADBifunctional protein PutA/0.468
4i8zG08Gag-Pol polyprotein3.4.23.160.467
1dirNADDihydropteridine reductase1.5.1.340.465
2znnS44Peroxisome proliferator-activated receptor alpha/0.465
1f20FADNitric oxide synthase, brain1.14.13.390.463
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.463
2ifaFMNUncharacterized protein/0.462
3oafOAGDihydrofolate reductase1.5.1.30.461
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.461
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.458
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.458
1xe55FEPlasmepsin-23.4.23.390.457
2b8l5HABeta-secretase 13.4.23.460.457
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.457
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.457
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.457
1xddAAYIntegrin alpha-L/0.456
3b70NAPEnoyl reductase LovC10.456
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.456
2oapANPType II secretion system protein (GspE-2)/0.455
3bbrBHYGlutamate receptor 2/0.455
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.455
4m4922YL-lactate dehydrogenase A chain1.1.1.270.455
5itzGTPTubulin alpha-1B chain/0.455
1lbcCYZGlutamate receptor 2/0.454
1me6IVSPlasmepsin-23.4.23.390.454
1tqf32PBeta-secretase 13.4.23.460.454
2cgv3B3Serine/threonine-protein kinase Chk12.7.11.10.454
3tjzGNPADP-ribosylation factor 1/0.454
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.454
2q4bNAPUncharacterized protein At5g02240/0.453
2iyfERYOleandomycin glycosyltransferase2.4.10.452
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.452
3in6FMNUncharacterized protein/0.452
3ziuLSSLeucyl-tRNA synthetase/0.452
2gjlFMNNitronate monooxygenase1.13.12.160.451
2hfuMEVMevalonate kinase/0.451
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.451
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.451
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.450
3d4pNADL-lactate dehydrogenase 11.1.1.270.450
3fwiCAMCamphor 5-monooxygenase1.14.15.10.450
4dptAGSMevalonate diphosphate decarboxylase/0.450
4jl5ADPAdenylate kinase/0.450
4djhJDCKappa-type opioid receptor/0.450
1t2cNAIL-lactate dehydrogenase1.1.1.270.449
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.449
1k8y13PTryptophan synthase alpha chain/0.448
1udaUFGUDP-glucose 4-epimerase5.1.3.20.448
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.448
2givACOHistone acetyltransferase KAT8/0.448
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.448
4f5yC2EStimulator of interferon genes protein/0.448
4ipw1G7Mycocyclosin synthase1.14.21.90.448
2he5NDPAldo-keto reductase family 1 member C211.1.10.447
2qblCAMCamphor 5-monooxygenase1.14.15.10.447
2rh9IGPTryptophan synthase alpha chain/0.447
2rhgIGPTryptophan synthase alpha chain/0.447
3q43D66M1 family aminopeptidase3.4.110.447
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.447
1bdlIM1Gag-Pol polyprotein3.4.23.160.446
1dr3HBIDihydrofolate reductase1.5.1.30.446
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.446
1lf2R37Plasmepsin-23.4.23.390.446
2a94AP0L-lactate dehydrogenase1.1.1.270.446
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.446
1yqzCOACoenzyme A disulfide reductase/0.445
2a9y26AAdenosine kinase2.7.1.200.445
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.445
2zjmF1MBeta-secretase 13.4.23.460.445
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.445
4l4dCAMCamphor 5-monooxygenase1.14.15.10.445
1beuIPLTryptophan synthase alpha chain/0.444
1rd7FOLDihydrofolate reductase1.5.1.30.444
1xvaSAMGlycine N-methyltransferase2.1.1.200.444
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.444
2znpK55Peroxisome proliferator-activated receptor delta/0.444
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.444
3t3r9PLCytochrome P450 2A61.14.130.444
3vt7VDXVitamin D3 receptor/0.444
1bxoPP7Penicillopepsin-13.4.23.200.443
1jipKTN6-deoxyerythronolide B hydroxylase/0.443
1nooCAHCamphor 5-monooxygenase1.14.15.10.443
3tdj3TJGlutamate receptor 2/0.443
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1hdrNADDihydropteridine reductase1.5.1.340.442
2gz8F3FOrf1a polyprotein/0.442
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.442
3tneRITCandidapepsin-13.4.23.240.442
4prvADPDNA gyrase subunit B/0.442
1jolFFODihydrofolate reductase1.5.1.30.441
1xe65FPPlasmepsin-23.4.23.390.441
2e0nSAHPrecorrin-2 C20-methyltransferase/0.441
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
3vqsJT1Genome polyprotein/0.441
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.441
1dr2TAPDihydrofolate reductase1.5.1.30.440
1drhNAPDihydrofolate reductase1.5.1.30.440
1yrcCAMCamphor 5-monooxygenase1.14.15.10.440
2g1o2IGRenin3.4.23.150.440
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.440
3nl6TPSUncharacterized protein/0.440
3s3vTOPDihydrofolate reductase1.5.1.30.440
4g95OAGDihydrofolate reductase1.5.1.30.440