sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3fvp | UB2 | Thermolysin | 3.4.24.27 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3fvp | UB2 | Thermolysin | 3.4.24.27 | 1.000 | |
| 1u4g | HPI | Elastase | 3.4.24.26 | 0.560 | |
| 3fv4 | 1U4 | Thermolysin | 3.4.24.27 | 0.522 | |
| 3f2p | S3B | Thermolysin | 3.4.24.27 | 0.508 | |
| 3f28 | S7B | Thermolysin | 3.4.24.27 | 0.500 | |
| 3fgd | BYA | Thermolysin | 3.4.24.27 | 0.485 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.476 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.465 | |
| 5a8a | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.465 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.464 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.464 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 1pw6 | FRB | Interleukin-2 | / | 0.458 | |
| 4cth | RDF | Neprilysin | / | 0.456 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.456 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.456 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.454 | |
| 2x93 | X93 | Angiotensin-converting enzyme | 3.4.15.1 | 0.453 | |
| 4zr5 | RDF | Neprilysin | / | 0.453 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.453 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.452 | |
| 3zuk | RDF | Endopeptidase, peptidase family M13 | / | 0.452 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.451 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.451 | |
| 4o0m | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.451 | |
| 4tmn | 0PK | Thermolysin | 3.4.24.27 | 0.451 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.450 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 4h6p | FMN | Chromate reductase | / | 0.450 | |
| 2e20 | B4P | Propionate kinase | / | 0.449 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.449 | |
| 1ao0 | 5GP | Amidophosphoribosyltransferase | / | 0.448 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.448 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.448 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.446 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.446 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.446 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.446 | |
| 3dwb | RDF | Endothelin-converting enzyme 1 | 3.4.24.71 | 0.446 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.445 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.444 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.443 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.443 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.441 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.441 | |
| 3eld | SFG | Methyltransferase | / | 0.441 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.441 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 1dd6 | MCI | Metallo-beta-lactamase type 2 | / | 0.440 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2j08 | IRF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.440 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.440 | |
| 4xmx | BES | Aminopeptidase N | 3.4.11.2 | 0.440 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.440 | |
| 5c3r | HMU | Thymine dioxygenase | / | 0.440 |