sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2onf | COA | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2onf | COA | Uncharacterized protein | / | 1.000 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.501 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.501 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.482 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.477 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.473 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.465 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.464 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.464 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.464 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4h0v | NAD | Iota toxin component Ia | / | 0.463 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.461 | |
| 1n0s | FLU | Bilin-binding protein | / | 0.460 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.460 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.460 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.460 | |
| 1qs2 | NAD | Vip2Ac | / | 0.460 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.459 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.459 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.458 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.457 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.457 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.457 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.456 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.455 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.454 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.453 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.453 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.453 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.452 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.452 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.452 | |
| 2qmz | LDP | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.452 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.452 | |
| 5dp2 | NAP | CurF | / | 0.452 | |
| 1lke | DOG | Bilin-binding protein | / | 0.451 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.451 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.451 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.450 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.448 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.448 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.448 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 4kxj | P34 | Nucleoprotein | / | 0.448 | |
| 2pdl | TOL | Aldose reductase | 1.1.1.21 | 0.447 | |
| 3sfx | JAN | Uncharacterized protein | / | 0.447 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.447 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.447 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.446 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.446 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.446 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.444 | |
| 1swe | BTN | Streptavidin | / | 0.444 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.444 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1zdw | FLV | Prenyltransferase | / | 0.443 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 5cuq | NSC | Genome polyprotein | / | 0.443 | |
| 1tys | DHF | Thymidylate synthase | / | 0.442 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2r96 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.442 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.442 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.442 | |
| 4j7h | TRH | PCZA361.3 | / | 0.442 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.442 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.442 | |
| 1ddt | APU | Diphtheria toxin | / | 0.441 | |
| 1jf0 | CZH | Obelin | / | 0.441 | |
| 1x2e | ATX | Proline iminopeptidase | 3.4.11.5 | 0.441 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3f0r | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.441 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 4lng | JAN | CaaX farnesyltransferase beta subunit Ram1 | / | 0.441 | |
| 4x9d | U5P | Uncharacterized protein MJ1435 | / | 0.441 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 2rbe | ZMG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3uhm | RFN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.440 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 4jyz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.440 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.440 |