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 |
|---|---|---|---|
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 1.000 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.607 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.597 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.562 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.528 | |
| 2emu | SAH | Diphthine synthase | / | 0.483 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.481 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.476 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.475 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.474 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.474 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.474 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 2dsg | SAH | Diphthine synthase | / | 0.472 | |
| 2ejz | SAH | Diphthine synthase | / | 0.470 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.469 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.468 | |
| 1vce | SAH | Diphthine synthase | / | 0.468 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.465 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2o12 | FMN | Chorismate synthase | / | 0.464 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.464 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.463 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.462 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.462 | |
| 2owk | SAH | Diphthine synthase | / | 0.462 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.462 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.461 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.461 | |
| 2ejk | SAH | Diphthine synthase | / | 0.461 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.461 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.460 | |
| 2e08 | SAH | Diphthine synthase | / | 0.460 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.460 | |
| 2pci | SAH | Diphthine synthase | / | 0.460 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.459 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 4dja | FAD | (6-4) photolyase | / | 0.459 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.459 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.458 | |
| 2hut | SAH | Diphthine synthase | / | 0.458 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.458 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.458 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.458 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.457 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.457 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.457 | |
| 1fml | RTL | Retinol dehydratase | / | 0.456 | |
| 2e17 | SAH | Diphthine synthase | / | 0.456 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.456 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.456 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.456 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.456 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.456 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.455 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.455 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.455 | |
| 2dxw | SAH | Diphthine synthase | / | 0.454 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.454 | |
| 3iaa | TYD | CalG2 | / | 0.454 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.453 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.452 | |
| 2e7r | SAH | Diphthine synthase | / | 0.452 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.452 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.452 | |
| 4xr9 | NAD | CalS8 | / | 0.452 | |
| 2ehl | SAH | Diphthine synthase | / | 0.451 | |
| 2p6l | SAH | Diphthine synthase | / | 0.451 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.451 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4pd6 | URI | Nucleoside permease | / | 0.450 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.449 | |
| 1r2j | FAD | FkbI | / | 0.449 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.449 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.449 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.449 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.449 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.449 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.449 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.448 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.448 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 2e8q | SAH | Diphthine synthase | / | 0.448 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.448 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2z6r | SAH | Diphthine synthase | / | 0.448 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.448 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.448 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.447 | |
| 2el0 | SAH | Diphthine synthase | / | 0.447 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.447 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.447 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.447 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.447 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.447 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.447 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.447 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.446 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.446 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.446 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2jcx | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.446 | |
| 3a3g | DLZ | Lumazine protein | / | 0.446 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.446 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.446 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.445 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.445 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.445 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.445 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.444 | |
| 2dxv | SAH | Diphthine synthase | / | 0.444 | |
| 2e8r | SAH | Diphthine synthase | / | 0.444 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.444 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.444 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 5a3b | APR | SIR2 family protein | / | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.443 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.443 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.443 | |
| 2p6k | SAH | Diphthine synthase | / | 0.443 | |
| 2pcg | SAH | Diphthine synthase | / | 0.443 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.443 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.443 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4ho9 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.443 | |
| 4jic | FMN | GTN Reductase | / | 0.443 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.443 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.443 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 2dsi | SAH | Diphthine synthase | / | 0.442 | |
| 2p5f | SAH | Diphthine synthase | / | 0.442 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.442 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.442 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.442 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.441 | |
| 2e8h | SAH | Diphthine synthase | / | 0.441 | |
| 2owg | SAH | Diphthine synthase | / | 0.441 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.441 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.441 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.441 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4lht | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.441 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1n3r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.440 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2e07 | SAH | Diphthine synthase | / | 0.440 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.440 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.440 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.440 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.440 | |
| 4bqh | 9VU | UDP-N-acetylglucosamine pyrophosphorylase, putative | / | 0.440 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.440 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.440 | |
| 4umx | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 |