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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
1pvgANPDNA topoisomerase 25.99.1.3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1pvgANPDNA topoisomerase 25.99.1.31.000
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.660
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.638
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.635
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.504
3h4lANPDNA mismatch repair protein PMS1/0.501
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.496
1nhhANPDNA mismatch repair protein MutL/0.490
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.468
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.464
1z5aADPType 2 DNA topoisomerase 6 subunit B/0.461
1g1aNADdTDP-glucose 4,6-dehydratase/0.460
4xcjADPHeat shock cognate 90 kDa protein/0.455
3u9eCOALmo1369 protein/0.454
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.454
3imgBZ2Pantothenate synthetase6.3.2.10.453
1nzdUPGDNA beta-glucosyltransferase/0.452
1thnADPAnti-sigma F factor/0.452
4a8v2ANMajor pollen allergen Bet v 1-J/0.452
4qxp1YEStimulator of interferon genes protein/0.451
1kqcFMNOxygen-insensitive NAD(P)H nitroreductase/0.450
4ivgANPTNF receptor-associated protein 1/0.449
4wudANPDNA gyrase subunit B/0.449
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.449
4a802ANMajor pollen allergen Bet v 1-A/0.448
4egbNADdTDP-glucose 4,6-dehydratase/0.448
4g7gVFVLanosterol 14-alpha-demethylase/0.448
3qt62P0Mevalonate diphosphate decarboxylase/0.447
4ipeANPTNF receptor-associated protein 1/0.447
4xclAGSHeat shock cognate 90 kDa protein/0.447
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.445
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.445
3gnvXNZGenome polyprotein2.7.7.480.445
4z24FADPutative GMC-type oxidoreductase R13510.444
1i59ANPChemotaxis protein CheA2.7.13.30.443
3lqfNADGalactitol dehydrogenase/0.443
4dc0NDPPutative ketoacyl reductase1.3.10.443
4y9qC2EUncharacterized protein/0.443
1xe65FPPlasmepsin-23.4.23.390.442
3qwbNDPProbable quinone oxidoreductase1.6.5.50.442
4prvADPDNA gyrase subunit B/0.442
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2gjlFMNNitronate monooxygenase1.13.12.160.441
3djjFADGlutathione reductase, mitochondrial1.8.1.70.441
3pm1ETHTH-type transcriptional regulator QacR/0.441
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.441
4wucANPDNA gyrase subunit B/0.441
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1k7fIAVTryptophan synthase alpha chain/0.440
2gmjFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.440
2ifaFMNUncharacterized protein/0.440
3sf6FDAGlutaryl-CoA dehydrogenase/0.440
4bfzZVZPantothenate kinase2.7.1.330.440
4dpuAGSMevalonate diphosphate decarboxylase/0.440
4jc51K5Stimulator of interferon genes protein/0.440
4prxADPDNA gyrase subunit B/0.440