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 |
|---|---|---|---|
| 4a39 | GEM | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4a39 | GEM | Uncharacterized protein | / | 1.000 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.494 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.481 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.476 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.467 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.467 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.465 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.465 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 4kxj | P34 | Nucleoprotein | / | 0.464 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.460 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1wp4 | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.454 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.454 | |
| 2z78 | H86 | Geranylgeranyl pyrophosphate synthase | / | 0.454 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 4in4 | 4ID | Kelch-like ECH-associated protein 1 | / | 0.454 | |
| 1krv | 147 | Galactoside O-acetyltransferase | 2.3.1.18 | 0.453 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.453 | |
| 2xej | OKD | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.453 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.452 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.451 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.450 | |
| 2xeg | CI9 | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.450 | |
| 2y5s | 78H | Dihydropteroate synthase | / | 0.450 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.450 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.449 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.449 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.448 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2e8t | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.448 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.448 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.448 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.447 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1z0s | ATP | NAD kinase | / | 0.446 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.446 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.445 | |
| 3thr | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.445 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.443 | |
| 4kqw | NAP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.443 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.442 | |
| 1dfo | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.442 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.442 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.442 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.441 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.440 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.440 |