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 |
|---|---|---|---|
| 1cg0 | IMO | Adenylosuccinate synthetase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1cg0 | IMO | Adenylosuccinate synthetase | / | 1.000 | |
| 1cg1 | IMO | Adenylosuccinate synthetase | / | 0.631 | |
| 1cg3 | IMO | Adenylosuccinate synthetase | / | 0.613 | |
| 1qf5 | RPL | Adenylosuccinate synthetase | / | 0.596 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.589 | |
| 2gcq | DOI | Adenylosuccinate synthetase | / | 0.588 | |
| 1cg4 | IMO | Adenylosuccinate synthetase | / | 0.583 | |
| 1p9b | IMO | Adenylosuccinate synthetase | / | 0.575 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.563 | |
| 1lon | IMO | Adenylosuccinate synthetase isozyme 1 | / | 0.562 | |
| 1ksz | PGS | Adenylosuccinate synthetase | / | 0.551 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.548 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.512 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.482 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.481 | |
| 2qn7 | HBZ | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.479 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.479 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.478 | |
| 3zcs | CAW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.478 | |
| 5dp2 | NAP | CurF | / | 0.478 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.476 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.475 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.473 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.473 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.472 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.472 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.472 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.471 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.471 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.470 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.469 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.469 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.469 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.468 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.466 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.466 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.466 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.466 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.465 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.465 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.465 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.465 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.465 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.464 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.463 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.462 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.461 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.461 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.461 | |
| 4l4x | NDP | AmphI | / | 0.461 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.460 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.460 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.460 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.460 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.460 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.460 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.459 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.459 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.459 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.458 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.458 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.458 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.457 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.457 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.457 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.456 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.456 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.455 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.455 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.455 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.455 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.454 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.454 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.453 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.453 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.453 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.453 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.453 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.453 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.453 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.452 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.452 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.452 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.452 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.452 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.451 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.451 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.451 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.451 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.451 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.451 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.451 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.450 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.450 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.450 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 4die | C5P | Cytidylate kinase | / | 0.450 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.450 | |
| 4qxp | 1YE | Stimulator of interferon genes protein | / | 0.450 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 2fze | APR | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.449 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.449 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.449 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.448 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.448 | |
| 4qec | NAP | ElxO | / | 0.448 | |
| 5dmh | ADP | 3-oxo-tetronate kinase | / | 0.448 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 2y3s | TIR | TamL | / | 0.447 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.447 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.446 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.446 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.446 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.446 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.445 | |
| 1nvm | NAD | Acetaldehyde dehydrogenase | 1.2.1.10 | 0.445 | |
| 1sny | NAP | LD36273p | / | 0.445 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.445 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.444 | |
| 1okk | GCP | Signal recognition particle protein | / | 0.444 | |
| 1okk | GCP | Signal recognition particle receptor FtsY | / | 0.444 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.444 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.444 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.444 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.444 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.443 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.443 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.443 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.443 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.443 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.443 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.443 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.443 | |
| 5a3b | APR | SIR2 family protein | / | 0.443 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.442 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.442 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.442 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.442 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.442 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.441 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.441 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.441 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.441 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.441 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.441 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.441 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.441 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.441 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.441 | |
| 5a3c | NAD | SIR2 family protein | / | 0.441 | |
| 5epo | TUD | 7-alpha-hydroxysteroid deydrogenase | / | 0.441 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.440 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.440 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.440 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.440 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.440 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.440 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.440 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.440 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.440 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.440 | |
| 4kqw | NAP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.440 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.440 |