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 |
|---|---|---|---|
| 3ngq | 1PS | CCR4-NOT transcription complex subunit 6-like | 3.1.13.4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ngq | 1PS | CCR4-NOT transcription complex subunit 6-like | 3.1.13.4 | 1.000 | |
| 5dv2 | C5P | CCR4-NOT transcription complex subunit 6-like | 3.1.13.4 | 0.569 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.475 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.466 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.466 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.466 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.460 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.460 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.457 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.457 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.457 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.456 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.455 | |
| 5il1 | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.453 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.451 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.451 | |
| 2xpc | 051 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.451 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.450 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.450 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.449 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.449 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.448 | |
| 1tys | DHF | Thymidylate synthase | / | 0.448 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.448 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.448 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.447 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.446 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.445 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1g28 | FMN | PHY3 | / | 0.444 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.444 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.444 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.443 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.442 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.441 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.441 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 3v2u | ATP | Protein GAL3 | / | 0.440 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.440 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.440 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.440 |