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 |
|---|---|---|---|
| 1g16 | GDP | Ras-related protein SEC4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1g16 | GDP | Ras-related protein SEC4 | / | 1.000 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.503 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.498 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.498 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.491 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.489 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.483 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.480 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.480 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.478 | |
| 1a4r | GNH | Cell division control protein 42 homolog | / | 0.476 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.470 | |
| 4l9s | GDP | GTPase HRas | / | 0.468 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.467 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.466 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.463 | |
| 2msd | GNP | MHC class I alpha chain | / | 0.463 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.463 | |
| 1q6t | 600 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.461 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.461 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.459 | |
| 4luc | GDP | GTPase KRas | / | 0.459 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.458 | |
| 4h1v | GNP | Dynamin-1-like protein | 3.6.5.5 | 0.458 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.458 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.457 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.457 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.455 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.454 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.454 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.454 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.453 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.453 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1q6s | 214 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.452 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.452 | |
| 3l8y | GNP | GTPase HRas | / | 0.452 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.452 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.451 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.451 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.451 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.451 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.451 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.451 | |
| 5b2z | GNP | GTPase HRas | / | 0.451 | |
| 5li5 | THR_ALA_ASN_PRO_SEP | KLTH0G14146p | / | 0.451 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.450 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.450 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.450 | |
| 3tgp | GNP | GTPase HRas | / | 0.450 | |
| 4hi0 | GDP | Urease accessory protein UreG | / | 0.450 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.450 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.449 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1bp6 | UMP | Thymidylate synthase | / | 0.448 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.448 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.448 | |
| 3rs7 | GNP | GTPase HRas | / | 0.448 | |
| 4mit | GTP | Rho-related protein racC | / | 0.448 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.447 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.446 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.446 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.446 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.446 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.446 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.446 | |
| 5cdt | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.445 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.445 | |
| 2vht | ATP | NTPase P4 | / | 0.445 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.445 | |
| 4tq9 | GDP | GTPase KRas | / | 0.445 | |
| 5jjs | SAH | Genome polyprotein | / | 0.445 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.444 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3clx | X22 | E3 ubiquitin-protein ligase XIAP | 6.3.2 | 0.444 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.444 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.444 | |
| 4blr | UTP | NTPase P4 | / | 0.444 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.443 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.443 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.443 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 3ieu | GDP | GTPase Era | / | 0.443 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.443 | |
| 3lbn | GNP | GTPase HRas | / | 0.443 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.443 | |
| 4kos | 4KO | Uncharacterized protein | / | 0.443 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.443 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.442 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 3rs5 | GNP | GTPase HRas | / | 0.442 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.442 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.442 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.442 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.441 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.441 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.441 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.441 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3eku | CY9 | Actin-5C | / | 0.441 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.441 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3wag | TYD | Glycosyltransferase | / | 0.441 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1az2 | NAP | Aldose reductase | 1.1.1.21 | 0.440 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.440 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.440 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.440 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.440 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 | |
| 4nxx | GDP | Mitochondrial dynamics protein MID51 | / | 0.440 |