sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1m8k | NAD | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1m8k | NAD | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 1.000 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.499 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.490 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.489 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.484 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.482 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.482 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.482 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.476 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.475 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.474 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.472 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.472 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.468 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.468 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.468 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.467 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.467 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.467 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.466 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.464 | |
| 4jic | FMN | GTN Reductase | / | 0.464 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.463 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.462 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.461 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.461 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.460 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.460 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.460 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.459 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.459 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.459 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.458 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.457 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.457 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.456 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.455 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.455 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.455 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3u9e | COA | Lmo1369 protein | / | 0.454 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.454 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.453 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.453 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.453 | |
| 3ag6 | PAJ | Pantothenate synthetase | / | 0.453 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.453 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.453 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.452 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.451 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.451 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.451 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.451 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.451 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.451 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.451 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.450 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.450 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.450 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.450 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.450 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.450 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.449 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.449 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.449 | |
| 4nau | AGS | Phosphopantetheine adenylyltransferase | / | 0.449 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.448 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.448 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.448 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.448 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.448 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.448 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.447 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.447 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.447 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.447 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.447 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.447 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.447 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.446 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.446 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.446 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.445 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.445 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.445 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.445 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.445 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.444 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.444 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.444 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.444 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.444 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.443 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.443 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.442 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
| 4iae | 1DX | Alr2278 protein | / | 0.442 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.442 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.442 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.442 | |
| 1s07 | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.441 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.441 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.441 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.441 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4g6g | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.441 | |
| 1ej2 | NAD | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.440 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.440 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.440 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.440 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.440 | |
| 2udp | UPP | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 3coz | 54H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3hf3 | FMN | Chromate reductase | / | 0.440 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.440 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4jky | ADP | Adenylate kinase | / | 0.440 |