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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
3dolGWIPol protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3dolGWIPol protein/1.000
3e01PZ2Gag-Pol polyprotein2.7.7.490.618
3dyaPZLGag-Pol polyprotein2.7.7.490.606
4h4o506Gag-Pol polyprotein2.7.7.490.595
3c6tM14Gag-Pol polyprotein2.7.7.490.593
1rtiHEFGag-Pol polyprotein2.7.7.490.592
4h4m494Gag-Pol polyprotein2.7.7.490.591
3t1a5MAGag-Pol polyprotein2.7.7.490.581
3dmjGWEPol protein/0.580
3ffi3OBGag-Pol polyprotein2.7.7.490.577
3c6uM22Gag-Pol polyprotein2.7.7.490.575
1jlaTNKGag-Pol polyprotein2.7.7.490.570
2be2R22Gag-Pol polyprotein2.7.7.490.563
1s1vTNKGag-Pol polyprotein2.7.7.490.562
3lakKR1Gag-Pol polyprotein2.7.7.490.561
3dlgGWEGag-Pol polyprotein2.7.7.490.556
3t195MAGag-Pol polyprotein2.7.7.490.556
1rt2TNKGag-Pol polyprotein2.7.7.490.555
3dokGWJPol protein/0.551
3dleGFAGag-Pol polyprotein2.7.7.490.550
4i7fNVEGag-Pol polyprotein2.7.7.490.549
3i0rRT3Gag-Pol polyprotein2.7.7.490.541
1c1bGCAGag-Pol polyprotein2.7.7.490.540
4mfb29TGag-Pol polyprotein2.7.7.490.540
3is9AC7Gag-Pol polyprotein2.7.7.490.537
1klmSPPGag-Pol polyprotein2.7.7.490.534
4rw4494Gag-Pol polyprotein2.7.7.490.534
3drpR8EGag-Pol polyprotein2.7.7.490.533
3lamKRPGag-Pol polyprotein2.7.7.490.530
1c1c612Gag-Pol polyprotein2.7.7.490.525
1ep4S11Gag-Pol polyprotein2.7.7.490.524
3di6PDZGag-Pol polyprotein2.7.7.490.522
3drrR8EGag-Pol polyprotein2.7.7.490.522
3i0sRT7Gag-Pol polyprotein2.7.7.490.518
1rt1MKCGag-Pol polyprotein2.7.7.490.514
3lanKBTGag-Pol polyprotein2.7.7.490.509
2rkiTT1Gag-Pol polyprotein2.7.7.490.505
2wonZZEGag-Pol polyprotein2.7.7.490.505
2ynhEURGag-Pol polyprotein2.7.7.490.500
3tamM06Gag-Pol polyprotein2.7.7.490.492
1hpzAAPGag-Pol polyprotein2.7.7.490.489
3nbpJGZGag-Pol polyprotein2.7.7.490.486
2ynfWHUGag-Pol polyprotein2.7.7.490.485
1fmjRTLRetinol dehydratase/0.483
1hquHBYGag-Pol polyprotein2.7.7.490.478
1fmlRTLRetinol dehydratase/0.474
5cyqT27Gag-Pol polyprotein2.7.7.490.472
1tvrTB9Gag-Pol polyprotein2.7.7.490.468
3t2yFADSulfide-quinone reductase/0.467
3m8qDJZGag-Pol polyprotein2.7.7.490.465
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.465
1yc2NADNAD-dependent protein deacylase 2/0.464
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
2ic3HBYGag-Pol polyprotein2.7.7.490.463
4nc3ERM5-hydroxytryptamine receptor 2B/0.463
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.461
2wetFADTryptophan 5-halogenase/0.459
2zbaZBATrichothecene 3-O-acetyltransferase/0.459
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.459
2jn3JN3Fatty acid-binding protein, liver/0.457
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.457
3lalKRVGag-Pol polyprotein2.7.7.490.457
3vrwYS5Vitamin D3 receptor/0.456
4jqeANPCasein kinase II subunit alpha2.7.11.10.456
4j6cSTRCytochrome P450 monooxygenase/0.453
1aq1STUCyclin-dependent kinase 22.7.11.220.452
2q5g1FAPeroxisome proliferator-activated receptor delta/0.452
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.452
3p3zP3ZPutative cytochrome P450/0.452
1m13HYFNuclear receptor subfamily 1 group I member 2/0.451
2w0bCMWLanosterol 14-alpha demethylase1.14.13.700.451
2zlaVDBVitamin D3 receptor/0.451
4iui1GQEstrogen receptor/0.451
2j14GNIPeroxisome proliferator-activated receptor delta/0.450
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.450
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
2iw94SPCyclin-dependent kinase 22.7.11.220.449
3uovFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.449
4ia2BIVVitamin D3 receptor A/0.449
4xldBRLPeroxisome proliferator-activated receptor gamma/0.449
1rkhVD2Vitamin D3 receptor/0.448
2ardFDAFlavin-dependent tryptophan halogenase PrnA1.14.19.90.448
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4z44FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.448
1ju6LYAThymidylate synthase2.1.1.450.447
2y60M8FIsopenicillin N synthase1.21.3.10.447
3u8hBHPPhospholipase A2, membrane associated/0.447
4dhyS41Glucokinase2.7.1.20.447
4uymVOR14-alpha sterol demethylase Cyp51B/0.447
2hb7O1CVitamin D3 receptor/0.446
3mnrSD1Heat shock protein HSP 90-alpha/0.446
3tmz06XCytochrome P450 2B41.14.14.10.446
4h9506UDihydrofolate reductase1.5.1.30.446
5hs1VORLanosterol 14-alpha demethylase/0.446
1v7aFRCAdenosine deaminase3.5.4.40.445
2hasC3OVitamin D3 receptor/0.445
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.445
3vrtYS2Vitamin D3 receptor/0.445
4rupH97Vitamin D3 receptor A/0.445
1hniAAAGag-Pol polyprotein2.7.7.490.444
2wi72KLHeat shock protein HSP 90-alpha/0.444
3vt5YI2Vitamin D3 receptor/0.444
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.444
4ia1BIVVitamin D3 receptor A/0.444
1s7gNADNAD-dependent protein deacylase 2/0.443
1tl3H20Gag-Pol polyprotein2.7.7.490.443
2hnzPC0Gag-Pol polyprotein2.7.7.490.443
3kpkFADSulfide-quinone reductase/0.443
1xddAAYIntegrin alpha-L/0.442
2xlsFADPutative flavin-containing monooxygenase/0.442
3qly55VUncharacterized protein/0.442
3wv9FEGHmd co-occurring protein HcgE/0.442
4ia3BIVVitamin D3 receptor A/0.442
4ia7BIVVitamin D3 receptor A/0.442
4ead0NPThymidine phosphorylase2.4.2.40.441
4eilCB3Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.441
4g1z0VPVitamin D3 receptor A/0.441
4o71CPBBromodomain-containing protein 4/0.441
4pkl1GHUncharacterized protein/0.441
1vrwNAIEnoyl-ACP reductase/0.440
2hamC33Vitamin D3 receptor/0.440
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.440
2om9AJAPeroxisome proliferator-activated receptor gamma/0.440
3inxJZCHeat shock protein HSP 90-alpha/0.440
3r83Z14Cyclin-dependent kinase 22.7.11.220.440
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4d7eFADPutative lysine-N-oxygenase/0.440
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.440