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 |
|---|---|---|---|
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 | 1.000 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.504 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.503 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.497 | |
| 3x2e | NAI | Adenosylhomocysteinase | / | 0.492 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.491 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.486 | |
| 3tog | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.486 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.485 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.483 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.479 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.477 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.476 | |
| 3dm5 | GDP | Signal recognition particle 54 kDa protein | / | 0.476 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.471 | |
| 1hpx | KNI | Gag-Pol polyprotein | / | 0.469 | |
| 4h0y | LAR | Actin, alpha skeletal muscle | / | 0.469 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4mo4 | ACP | Anhydro-N-acetylmuramic acid kinase | / | 0.466 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.465 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.465 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.465 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.464 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.463 | |
| 2v1x | ADP | ATP-dependent DNA helicase Q1 | 3.6.4.12 | 0.463 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 3rk1 | ATP | N-type ATP pyrophosphatase superfamily | / | 0.463 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.463 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.463 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.462 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.462 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.462 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.462 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.461 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 5hg0 | SAM | Pantothenate synthetase | / | 0.460 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.458 | |
| 5aga | ANP | DNA polymerase theta | / | 0.458 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.458 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.457 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.457 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.457 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.457 | |
| 1n2j | PAF | Pantothenate synthetase | 6.3.2.1 | 0.456 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.456 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.455 | |
| 3h3c | P1E | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.455 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.455 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.455 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.454 | |
| 2iiq | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.454 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.454 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.454 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.454 | |
| 4aa5 | NQB | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.454 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 1k8y | 13P | Tryptophan synthase alpha chain | / | 0.453 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase | / | 0.453 | |
| 3omu | IBD | Heat shock protein 83 | / | 0.453 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.453 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.453 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.452 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.452 | |
| 2p3b | 3TL | V-1 protease | / | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 4kq1 | U5P | Glycogen [starch] synthase | / | 0.452 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.452 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.451 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.451 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.450 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.450 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.450 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.449 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.449 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.449 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.448 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.448 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.448 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.448 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.448 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.448 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.448 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.448 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.447 | |
| 1tw4 | CHD | Fatty acid-binding protein, liver | / | 0.447 | |
| 2i7n | ACO | Pantothenate kinase 1 | 2.7.1.33 | 0.447 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.447 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.447 | |
| 5dhh | DGW | Nociceptin receptor | / | 0.447 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.446 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.446 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.446 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.445 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.445 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3gue | UPG | UTP-glucose-1-phosphate uridylyltransferase 2, putative | / | 0.445 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.445 | |
| 3pwr | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4dja | FAD | (6-4) photolyase | / | 0.445 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.445 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.445 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.445 | |
| 4z87 | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.445 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.445 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.444 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 2f81 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 3wbb | NAP | Meso-diaminopimelate D-dehydrogenase | / | 0.444 | |
| 3zxs | FAD | Deoxyribodipyrimidine photolyase-related protein | / | 0.444 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.444 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1q1w | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.443 | |
| 1qr2 | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.443 | |
| 1wc4 | APC | Adenylate cyclase | / | 0.443 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.443 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.443 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.443 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3lb8 | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.443 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3uk6 | ADP | RuvB-like 2 | 3.6.4.12 | 0.443 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.443 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.443 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.442 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.442 | |
| 2yj4 | ATP | Copper-transporting ATPase | / | 0.442 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.442 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.441 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.441 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 2cmo | M1L | Glutamate receptor 2 | / | 0.441 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.441 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.441 | |
| 2x3f | APC | Pantothenate synthetase | / | 0.441 | |
| 3af2 | ACP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ua8 | 08W | Glutamate receptor 2 | / | 0.441 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.441 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4gav | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.441 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.441 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.441 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.441 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.440 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.440 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.440 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.440 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.440 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.440 | |
| 4kto | FAD | Putative isovaleryl-CoA dehydrogenase protein | / | 0.440 | |
| 4zvl | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 |