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 |
|---|---|---|---|
| 2yx6 | ADP | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2yx6 | ADP | Uncharacterized protein | / | 1.000 | |
| 2qg4 | NAD | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.496 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.485 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.485 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.473 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.472 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.467 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.465 | |
| 2fna | ADP | Uncharacterized protein | / | 0.464 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.463 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.462 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.461 | |
| 2bxm | IMN | Serum albumin | / | 0.461 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.460 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3qw4 | U5P | Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative | / | 0.460 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.459 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.458 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.458 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.458 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.457 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.457 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.456 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.456 | |
| 2xvv | 9DN | Serum albumin | / | 0.456 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.456 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.455 | |
| 4zrn | UPG | UDP-glucose 4-epimerase, putative | / | 0.455 | |
| 3eej | 53R | Uncharacterized protein | / | 0.454 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.454 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.454 | |
| 4g3q | UD1 | Bifunctional protein GlmU | / | 0.454 | |
| 4qxr | 1YE | Stimulator of interferon genes protein | / | 0.454 | |
| 4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.454 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.453 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.453 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.453 | |
| 2xvw | 9NR | Serum albumin | / | 0.453 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2ad5 | ADP | CTP synthase | / | 0.452 | |
| 2bun | FAD | AppA protein | / | 0.452 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.451 | |
| 2bxq | IMN | Serum albumin | / | 0.451 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.451 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.451 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.451 | |
| 3uwq | U5P | Orotidine 5'-phosphate decarboxylase | / | 0.451 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.450 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.450 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.450 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.450 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.450 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.449 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.449 | |
| 4k10 | NI9 | Farnesyl pyrophosphate synthase | / | 0.449 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.448 | |
| 1lrl | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.448 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.448 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.448 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.448 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.447 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.447 | |
| 3hko | ANP | Calcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands | / | 0.447 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.447 | |
| 4die | C5P | Cytidylate kinase | / | 0.447 | |
| 1ee0 | CAA | 2-pyrone synthase | / | 0.446 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.446 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.446 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.445 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.445 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.444 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.444 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.444 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.444 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.444 | |
| 3uoz | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.444 | |
| 1lol | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.443 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.443 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.443 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1e8h | ADP | Vanillyl-alcohol oxidase | 1.1.3.38 | 0.442 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.442 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.441 | |
| 1jvs | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.441 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.441 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 4ho9 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.441 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.441 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1z5c | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.440 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.440 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4k33 | ACP | Fibroblast growth factor receptor 3 | 2.7.10.1 | 0.440 | |
| 4z69 | DIF | Serum albumin | / | 0.440 |