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 |
|---|---|---|---|
| 4eep | FMN | Phototropin-2 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.000 | |
| 5efw | FMN | NPH1-1 | / | 0.586 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.569 | |
| 5djt | FMN | NPH1-2 | / | 0.569 | |
| 1g28 | FMN | PHY3 | / | 0.566 | |
| 5dkk | FMN | Predicted protein | / | 0.551 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.543 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.543 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.537 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.533 | |
| 4hj6 | FMN | LOV protein | / | 0.533 | |
| 2v1a | FMN | NPH1-1 | / | 0.527 | |
| 2v0u | FMN | NPH1-1 | / | 0.525 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.524 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.522 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.521 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.519 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.513 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.508 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.507 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.506 | |
| 4hia | FMN | LOV protein | / | 0.498 | |
| 3sw1 | FMN | Sensory box protein | / | 0.493 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.491 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.488 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.487 | |
| 2owu | SAH | Diphthine synthase | / | 0.482 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.482 | |
| 2ejz | SAH | Diphthine synthase | / | 0.475 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.474 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3ske | 054 | Genome polyprotein | 2.7.7.48 | 0.472 | |
| 3b9l | AZZ | Serum albumin | / | 0.471 | |
| 3zhs | TD6 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.471 | |
| 4hj4 | FMN | LOV protein | / | 0.471 | |
| 4ih7 | 1ER | Genome polyprotein | 2.7.7.48 | 0.471 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 2gc8 | 885 | Polyprotein | / | 0.470 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.469 | |
| 5dju | FMN | NPH1-2 | / | 0.469 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.468 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.466 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.466 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 2ejk | SAH | Diphthine synthase | / | 0.465 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 3e51 | N35 | Genome polyprotein | 2.7.7.48 | 0.463 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.461 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.460 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.460 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.460 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.460 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.460 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.459 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.459 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.459 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.459 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.459 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.459 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.458 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 2yj4 | ATP | Copper-transporting ATPase | / | 0.458 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.458 | |
| 4dxd | 9PC | Cell division protein FtsZ | / | 0.458 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.457 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.457 | |
| 2z6r | SAH | Diphthine synthase | / | 0.456 | |
| 3cso | XNI | Genome polyprotein | 2.7.7.48 | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.455 | |
| 2el0 | SAH | Diphthine synthase | / | 0.455 | |
| 2p5f | SAH | Diphthine synthase | / | 0.455 | |
| 3gnv | XNZ | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.455 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.454 | |
| 2owf | SAH | Diphthine synthase | / | 0.454 | |
| 4gt8 | ADP | Sensor protein VraS | 2.7.13.3 | 0.454 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.454 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.453 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.453 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.453 | |
| 1wng | SAH | Diphthine synthase | / | 0.452 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.452 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.452 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.452 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.451 | |
| 2emu | SAH | Diphthine synthase | / | 0.451 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.451 | |
| 3p2o | NAD | Bifunctional protein FolD | / | 0.451 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.450 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4d9e | LCS | D-cysteine desulfhydrase | / | 0.450 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.449 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.449 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.449 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.449 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.449 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.449 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.449 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.449 | |
| 2e8h | SAH | Diphthine synthase | / | 0.448 | |
| 2hut | SAH | Diphthine synthase | / | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.448 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1yvf | PH7 | Polyprotein | / | 0.447 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.447 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1i2c | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.446 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.446 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.446 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.445 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.445 | |
| 2p2q | PRX | Acetyl-coenzyme A synthetase | / | 0.445 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.445 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.445 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.445 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.444 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.444 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.444 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.444 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.443 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.443 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.443 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.443 | |
| 3wag | TYD | Glycosyltransferase | / | 0.443 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 1vce | SAH | Diphthine synthase | / | 0.442 | |
| 2bxq | IMN | Serum albumin | / | 0.442 | |
| 3ge6 | FMN | Nitroreductase | / | 0.442 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 3vjc | ZGA | Squalene synthase | 2.5.1.21 | 0.442 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.441 | |
| 2e4n | SAH | Diphthine synthase | / | 0.441 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 2xvv | 9DN | Serum albumin | / | 0.441 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.441 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.441 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.440 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.440 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.440 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.440 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.440 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.440 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.440 | |
| 4rqu | NAD | Alcohol dehydrogenase class-P | / | 0.440 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 |