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 |
|---|---|---|---|
| 3zid | GDP | Tubulin-like protein CetZ |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3zid | GDP | Tubulin-like protein CetZ | / | 1.000 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.594 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.494 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.487 | |
| 4ei7 | GDP | Plasmid replication protein RepX | / | 0.469 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 0.469 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.468 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.468 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.467 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.467 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.465 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.464 | |
| 4ca8 | 3ES | Angiotensin-converting enzyme | 3.4.15.1 | 0.463 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.463 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.463 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.461 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.461 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.461 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 0.460 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.460 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.459 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.457 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.456 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.456 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.456 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.455 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.453 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.453 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.452 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.452 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.452 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.451 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.451 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.451 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.451 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.449 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.448 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.448 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.448 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.447 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.447 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.447 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.447 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.446 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.445 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.445 | |
| 4h4u | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.445 | |
| 5a01 | 12V | O-glycosyltransferase | / | 0.445 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.444 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.444 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.444 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.444 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.443 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.443 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.442 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.442 | |
| 3iaa | TYD | CalG2 | / | 0.442 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.442 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.442 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.442 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.442 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.440 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.440 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.440 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 |