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 |
|---|---|---|---|
| 3ewd | MCF | Adenosine deaminase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3ewd | MCF | Adenosine deaminase, putative | / | 1.000 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.485 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.485 | |
| 2r5n | TPP | Transketolase 1 | / | 0.485 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.485 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.479 | |
| 1trk | TPP | Transketolase 1 | 2.2.1.1 | 0.479 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.479 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.477 | |
| 4ear | IM5 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.476 | |
| 1nbu | PH2 | Dihydroneopterin aldolase | / | 0.474 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.471 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.468 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.465 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.464 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.463 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.463 | |
| 3upt | TPP | Transketolase | / | 0.461 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.460 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.460 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.460 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.458 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.458 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2y3f | BTN | Streptavidin | / | 0.454 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.451 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.451 | |
| 2yhu | WHF | Pteridine reductase | / | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 1sre | HAB | Streptavidin | / | 0.448 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.448 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.448 | |
| 1swe | BTN | Streptavidin | / | 0.447 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.447 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.447 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.447 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.447 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.446 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.446 | |
| 1sri | DMB | Streptavidin | / | 0.445 | |
| 1uhh | CZP | Aequorin-2 | / | 0.445 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.445 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3v2u | ATP | Protein GAL3 | / | 0.445 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.444 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.444 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.444 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2zi5 | 3L1 | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.443 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.443 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.443 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 5fsi | 8DG | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.443 | |
| 1mra | APG | Mandelate racemase | / | 0.442 | |
| 1xh5 | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.442 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 3wzn | BTN | Streptavidin | / | 0.442 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.442 | |
| 1dtp | APU | Diphtheria toxin | / | 0.441 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1z5c | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.441 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.441 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1db5 | 6IN | Phospholipase A2, membrane associated | / | 0.440 | |
| 2yat | EEU | Estrogen receptor | / | 0.440 | |
| 3myt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.440 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.440 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.440 |