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 |
|---|---|---|---|
| 4h4b | 11H | Cytosolic purine 5'-nucleotidase | 3.1.3.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4h4b | 11H | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 1.000 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.488 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.488 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.483 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.472 | |
| 1s4o | GDP | Glycolipid 2-alpha-mannosyltransferase | / | 0.471 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.471 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.469 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.469 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.466 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.466 | |
| 4ovi | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.466 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.466 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.465 | |
| 4yaw | 2AM | NADPH--cytochrome P450 reductase | / | 0.465 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.464 | |
| 5dbv | COA | Aldehyde Dehydrogenase | / | 0.464 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 1exv | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.460 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.460 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.460 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.460 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.460 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.459 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.459 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.459 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.459 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.458 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.458 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.458 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.458 | |
| 1pl6 | 572 | Sorbitol dehydrogenase | 1.1.1.14 | 0.457 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.457 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.457 | |
| 3qvi | K95 | HAP protein | / | 0.457 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.457 | |
| 1qxo | FMN | Chorismate synthase | / | 0.456 | |
| 4lut | DCS | Alanine racemase | / | 0.456 | |
| 4qfx | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.456 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.455 | |
| 2ylt | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.455 | |
| 3rv7 | RVB | Salicylate synthase | / | 0.455 | |
| 4ztv | TA7 | Anthranilate phosphoribosyltransferase | / | 0.455 | |
| 4y0k | NAP | AntE | / | 0.454 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.453 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.452 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.452 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.452 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.452 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.451 | |
| 2h59 | 3OD | NAD-dependent protein deacetylase | / | 0.451 | |
| 2xgo | ZKD | Uncharacterized protein | / | 0.451 | |
| 3kc1 | 2T6 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.451 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.451 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.451 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 3zuy | TCH | Transporter | / | 0.451 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.451 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.450 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.450 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.450 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.450 | |
| 4ac0 | MIY | Tetracycline repressor protein class B from transposon Tn10 | / | 0.450 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.450 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.449 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.449 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.449 | |
| 3kr5 | BEY | M17 leucyl aminopeptidase | / | 0.449 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.449 | |
| 3r6c | 17N | Anthranilate phosphoribosyltransferase | / | 0.449 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.449 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.449 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.448 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.448 | |
| 4xiv | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.448 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.447 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.447 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.447 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.447 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.447 | |
| 5hvn | NAD | 3-dehydroquinate synthase | / | 0.447 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.446 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.446 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.446 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.445 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3e39 | FMN | Nitroreductase | / | 0.445 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.445 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.445 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 1cju | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cju | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.444 | |
| 1llq | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.444 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.444 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.444 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.444 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.444 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.443 | |
| 2ay3 | MPP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.443 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.443 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.443 | |
| 4ask | K0I | Lysine-specific demethylase 6B | 1.14.11 | 0.443 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.443 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3n10 | CMP | Adenylate cyclase 2 | / | 0.442 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.442 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.442 | |
| 4azm | T4B | Fatty acid-binding protein, epidermal | / | 0.442 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.442 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.442 | |
| 5dld | UD1 | UDP-N-Acetylglucosamine 2-epimerase | / | 0.442 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.441 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1l7x | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.441 | |
| 1z45 | UPG | Bifunctional protein GAL10 | 5.1.3.2 | 0.441 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.441 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.441 | |
| 3tlk | EB4 | Ferrienterobactin-binding periplasmic protein | / | 0.441 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.441 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.440 | |
| 1g7u | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2gyo | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.440 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.440 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.440 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 3q33 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.440 | |
| 3zhv | TDW | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.440 | |
| 4a7y | NHF | Aldos-2-ulose dehydratase | / | 0.440 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.440 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.440 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.440 |