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 |
|---|---|---|---|
| 5jdz | SAH | Methyl transferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5jdz | SAH | Methyl transferase | / | 1.000 | |
| 5je3 | SAH | Methyl transferase | / | 0.757 | |
| 5je4 | SAH | Methyl transferase | / | 0.637 | |
| 1pl6 | 572 | Sorbitol dehydrogenase | 1.1.1.14 | 0.487 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.482 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.479 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.478 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.473 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.471 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.467 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.466 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.465 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.464 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.463 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.462 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.462 | |
| 4jxr | ACO | Acetyltransferase | / | 0.462 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.462 | |
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.460 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.460 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.460 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.460 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.459 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.459 | |
| 4mvc | CDC | Choline-phosphate cytidylyltransferase A | / | 0.459 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1gvr | TNL | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.456 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.455 | |
| 1xvv | CCQ | L-carnitine CoA-transferase | / | 0.453 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.453 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.453 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.452 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.452 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.450 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.450 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.449 | |
| 4h0x | NAD | Iota toxin component Ia | / | 0.449 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.449 | |
| 4qfx | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.449 | |
| 1coz | CTP | Glycerol-3-phosphate cytidylyltransferase | 2.7.7.39 | 0.448 | |
| 1icv | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.448 | |
| 1qs2 | NAD | Vip2Ac | / | 0.448 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.448 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.448 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.447 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.447 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.446 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.445 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 4uz6 | SCR | Palmitoleoyl-protein carboxylesterase NOTUM | / | 0.445 | |
| 1kqc | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.444 | |
| 2jgb | MGT | Eukaryotic translation initiation factor 4E type 2 | / | 0.444 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4j7g | TRH | PCZA361.3 | / | 0.444 | |
| 4k39 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.444 | |
| 4kq1 | U5P | Glycogen [starch] synthase | / | 0.444 | |
| 5doz | NDP | JamJ | / | 0.444 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.443 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.443 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.443 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1yro | GDU | Beta-1,4-galactosyltransferase 1 | / | 0.442 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 2yx6 | ADP | Uncharacterized protein | / | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.441 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.441 | |
| 3lm8 | VIB | Thiamine pyrophosphokinase | 2.7.6.2 | 0.441 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.441 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.440 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.440 |