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 |
|---|---|---|---|
| 4yj2 | GTP | Tubulin alpha-1B chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 1.000 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.573 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.534 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.508 | |
| 3ryh | GTP | Tubulin alpha chain | / | 0.498 | |
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 0.497 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.495 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.491 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.486 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.486 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.484 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.482 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.481 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.476 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.476 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.475 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.474 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.474 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.474 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.474 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.474 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.472 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.472 | |
| 1n2j | PAF | Pantothenate synthetase | 6.3.2.1 | 0.471 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.471 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.470 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4o4i | GTP | Tubulin alpha-1B chain | / | 0.470 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.469 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.469 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.467 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.467 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.467 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.466 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.465 | |
| 3v2u | ATP | Protein GAL3 | / | 0.464 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.463 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.463 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.462 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.462 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.462 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.460 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.460 | |
| 1p4a | PCP | Pur operon repressor | / | 0.459 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.459 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.459 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.459 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.459 | |
| 4xr9 | NAD | CalS8 | / | 0.459 | |
| 1bwf | ATF | Glycerol kinase | / | 0.458 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.458 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.458 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.458 | |
| 3dm5 | GDP | Signal recognition particle 54 kDa protein | / | 0.458 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.458 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.457 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.457 | |
| 4o4l | GTP | Tubulin alpha-1B chain | / | 0.457 | |
| 2bab | FAD | Putative aminooxidase | / | 0.456 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.456 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.456 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.456 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.455 | |
| 1n2b | PAF | Pantothenate synthetase | 6.3.2.1 | 0.455 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.455 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.455 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.455 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.455 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.455 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.455 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.454 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 2bac | FAD | Putative aminooxidase | / | 0.454 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.454 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.454 | |
| 5hg0 | SAM | Pantothenate synthetase | / | 0.454 | |
| 5la6 | GTP | Tubulin alpha-1B chain | / | 0.454 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.453 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.453 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.453 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.452 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.452 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.452 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.452 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.451 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.451 | |
| 1l5s | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.450 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.450 | |
| 3mk6 | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.450 | |
| 3rfa | SAM | Dual-specificity RNA methyltransferase RlmN | / | 0.450 | |
| 4ba5 | PXG | Probable aminotransferase | / | 0.450 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.450 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.449 | |
| 1n2g | APC | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.449 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.449 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.449 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 0.449 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.448 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.448 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.448 | |
| 2wi5 | ZZ5 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3lnc | 5GP | Guanylate kinase | / | 0.448 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.448 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.448 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.448 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.447 | |
| 2o12 | FMN | Chorismate synthase | / | 0.447 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.447 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 4ffb | GTP | Tubulin alpha-1 chain | / | 0.447 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.446 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.446 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.446 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.446 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.445 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.445 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.445 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.445 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.445 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.444 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.443 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.443 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.443 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.443 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.443 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.443 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.443 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.443 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.442 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.442 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.442 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 5ftc | ADP | TPR domain protein | / | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1vza | UMP | Thymidylate synthase | / | 0.441 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.441 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.441 | |
| 3fsu | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.441 | |
| 3fvl | BHK | Carboxypeptidase A1 | 3.4.17.1 | 0.441 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.441 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.441 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4e2d | FMN | Dehydrogenase | / | 0.441 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 5ftf | ADP | TPR domain protein | / | 0.441 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.441 | |
| 1a5b | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.440 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.440 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.440 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.440 |