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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
3oumTOFToxoflavin degrading enzyme

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3oumTOFToxoflavin degrading enzyme/1.000
2fpcSCGStrictosidine synthase4.3.3.20.508
1u1d181Uridine phosphorylase2.4.2.30.489
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.475
1opbRETRetinol-binding protein 2/0.472
2bfaCB3Pteridine reductase 11.5.1.330.472
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.472
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.466
3h4vDVPPteridine reductase 11.5.1.330.466
3lalKRVGag-Pol polyprotein2.7.7.490.465
4zobLGCLin1840 protein/0.465
1kqwRTLCellular retinol-binding protein type II/0.463
3u8hBHPPhospholipase A2, membrane associated/0.463
3a1l2CCCytochrome P450/0.460
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.459
2bf7HBIPteridine reductase 11.5.1.330.459
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3lakKR1Gag-Pol polyprotein2.7.7.490.457
3tdkUPGUDP-glucose 6-dehydrogenase1.1.1.220.457
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.455
1ndzFR5Adenosine deaminase3.5.4.40.455
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.454
5k2bZMAAdenosine receptor A2a/0.454
1h35R01Squalene--hopene cyclase4.2.1.1290.453
1rszDIHPurine nucleoside phosphorylase2.4.2.10.453
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.453
1upw444Oxysterols receptor LXR-beta/0.453
2q3eUPGUDP-glucose 6-dehydrogenase1.1.1.220.453
4uofDATNucleoside diphosphate kinase/0.453
1v79FR7Adenosine deaminase3.5.4.40.452
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
3emlZMAAdenosine receptor A2a/0.452
1ndyFR3Adenosine deaminase3.5.4.40.451
1o6rR19Squalene--hopene cyclase4.2.1.1290.451
3nefPYVAbscisic acid receptor PYL1/0.451
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
1e92HBIPteridine reductase 11.5.1.330.450
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.450
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.450
5ckwANPUncharacterized protein/0.450
3qly55VUncharacterized protein/0.449
4uy6SAHHistidine N-alpha-methyltransferase/0.449
1l0lFMXCytochrome b/0.448
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
4kq2U5PGlycogen [starch] synthase isoform 22.4.1.110.448
2bfmTOPPteridine reductase 11.5.1.330.447
2w98P1ZProstaglandin reductase 21.3.1.480.447
3aosJH2Hemolymph juvenile hormone binding protein/0.447
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
4g1z0VPVitamin D3 receptor A/0.447
5dozNDPJamJ/0.447
5iu4ZMAAdenosine receptor A2a/0.447
1crbRTLRetinol-binding protein 1/0.446
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.446
2b5j3ACGag-Pol polyprotein2.7.7.490.446
2r0pK2CPutative FAD-monooxygenase/0.446
3vg9ZMAAdenosine receptor A2a/0.446
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.446
1h36R88Squalene--hopene cyclase4.2.1.1290.445
1sm2STUTyrosine-protein kinase ITK/TSK2.7.10.20.445
3dlgGWEGag-Pol polyprotein2.7.7.490.445
1kzjCB3Thymidylate synthase/0.444
3ghvGHCDihydrofolate reductase1.5.1.30.444
3vf60H6Glucokinase2.7.1.20.444
4dbuBT9Aldo-keto reductase family 1 member C3/0.444
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4jbsP52Endoplasmic reticulum aminopeptidase 23.4.110.444
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1u1gBBBUridine phosphorylase2.4.2.30.443
2gpvOHTEstrogen-related receptor gamma/0.443
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.443
5iubCLRAdenosine receptor A2a/0.443
5iu86DZAdenosine receptor A2a/0.443
1thnADPAnti-sigma F factor/0.442
1z6tADPApoptotic protease-activating factor 1/0.442
3gi2GHWDihydrofolate reductase1.5.1.30.442
3ipq965Oxysterols receptor LXR-alpha/0.442
3is9AC7Gag-Pol polyprotein2.7.7.490.442
5h8tRTLRetinol-binding protein 1/0.442
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
1zdwFLVPrenyltransferase/0.441
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.441
2r0g7CKPutative FAD-monooxygenase/0.441
3iiuPIDPeridinin-chlorophyll a-binding protein 1, chloroplastic/0.441
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.441
3vrbFTNSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.441
3vrbFTNCytochrome b-large subunit/0.441
5uviZMAAdenosine receptor A2a/0.441
1dljUGAUDP-glucose 6-dehydrogenase/0.440
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3gkjHC3Niemann-Pick C1 protein/0.440
3s41S41Glucokinase2.7.1.20.440
3v94WYQPhosphodiesterase/0.440
4lsjLSJGlucocorticoid receptor/0.440
5cc9DDFDihydrofolate reductase1.5.1.30.440