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 |
|---|---|---|---|
| 2v7t | SAH | 5'-fluoro-5'-deoxy-adenosine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2v7t | SAH | 5'-fluoro-5'-deoxy-adenosine synthase | / | 1.000 | |
| 2v7u | SAM | 5'-fluoro-5'-deoxy-adenosine synthase | / | 0.785 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.488 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.484 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.483 | |
| 2zbv | ADN | Uncharacterized protein | / | 0.479 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.478 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.478 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.473 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.473 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.472 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.472 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.471 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1t3z | CAO | Formyl-CoA:oxalate CoA-transferase | / | 0.467 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.466 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.466 | |
| 1vft | DCS | Alanine racemase | / | 0.465 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.464 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.463 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.462 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.461 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.461 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.461 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2ejz | SAH | Diphthine synthase | / | 0.459 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.459 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.459 | |
| 1vgq | CAO | Formyl-CoA:oxalate CoA-transferase | / | 0.458 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.458 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.456 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.456 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.456 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.455 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.454 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.454 | |
| 4e32 | DWN | Methyltransferase | / | 0.454 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.453 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.453 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.453 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.453 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1xi2 | CB1 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.452 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 1swg | BTN | Streptavidin | / | 0.451 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.451 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.451 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2y1w | 849 | Histone-arginine methyltransferase CARM1 | / | 0.450 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.450 | |
| 4zvm | DM2 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.450 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.449 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.449 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.449 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.448 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.448 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.448 | |
| 1sg0 | STL | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.447 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.447 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.447 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2rh1 | CAU | Beta-2 adrenergic receptor | / | 0.447 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.446 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.446 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.446 | |
| 3w5u | FAD | Ferredoxin | / | 0.446 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.446 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.446 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.446 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.446 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.445 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.445 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.445 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.445 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3ndj | JHZ | Methyltransferase | / | 0.445 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3ox3 | 4X4 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.444 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.444 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.444 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.444 | |
| 2wnb | C5P | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1 | 2.4.99.4 | 0.444 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.444 | |
| 3nhj | A2Z | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.444 | |
| 3oy0 | OY0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 4c36 | ZO9 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 4hh4 | SAH | CcbJ | / | 0.444 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 4tta | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.444 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.443 | |
| 3d2m | COA | Amino-acid acetyltransferase | / | 0.443 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.443 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.443 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.443 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.443 | |
| 1lke | DOG | Bilin-binding protein | / | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.442 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4o6f | SAH | N-lysine methyltransferase SMYD2 | / | 0.442 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.441 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3uxh | UXH | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.441 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.441 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.440 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.440 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3gc4 | AAQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.440 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4iix | 1EG | Microcin C7 self-immunity protein MccF | / | 0.440 | |
| 4kxj | P34 | Nucleoprotein | / | 0.440 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.440 |