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 |
|---|---|---|---|
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 | 1.000 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.631 | |
| 1b8o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.621 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.581 | |
| 1a9s | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.575 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.574 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.567 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.542 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.533 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.524 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.521 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.519 | |
| 1v48 | HA1 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.518 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.515 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.515 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.507 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.506 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.506 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.496 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.492 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.491 | |
| 1pf7 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.482 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 4ear | IM5 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.480 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.479 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.478 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.478 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.477 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.475 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.473 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.469 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.468 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.468 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.465 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.465 | |
| 3eku | CY9 | Actin-5C | / | 0.464 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.462 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.462 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.461 | |
| 2p4s | DIH | AGAP005945-PA | / | 0.461 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.461 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.461 | |
| 4jic | FMN | GTN Reductase | / | 0.461 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.460 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.460 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.458 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.458 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.456 | |
| 3k8o | 229 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.455 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.455 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.455 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.454 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.454 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.454 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.454 | |
| 4e2d | FMN | Dehydrogenase | / | 0.454 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.453 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.453 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.453 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.453 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.452 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.452 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.452 | |
| 3ske | 054 | Genome polyprotein | 2.7.7.48 | 0.452 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.452 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.451 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.451 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.450 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.450 | |
| 1ty8 | ADP | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.450 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.450 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.450 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.450 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.450 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.450 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.450 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.449 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.449 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.449 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.449 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.449 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.448 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.448 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.448 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.448 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.447 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.447 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.447 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.447 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.447 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 2a8y | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.446 | |
| 2e8q | SAH | Diphthine synthase | / | 0.446 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.446 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.446 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1cjw | COT | Serotonin N-acetyltransferase | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.445 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.445 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.445 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.445 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 2r5n | TPP | Transketolase 1 | / | 0.445 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.445 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.445 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.445 | |
| 3gnv | XNZ | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.445 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.445 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.444 | |
| 1nj6 | A5A | Proline--tRNA ligase | / | 0.444 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.444 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.443 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.443 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.442 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.442 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.442 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.442 | |
| 1dnp | MHF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.441 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.441 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.441 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.441 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.441 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4wfr | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.440 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2owf | SAH | Diphthine synthase | / | 0.440 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3t94 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.440 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.440 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.440 |