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 |
|---|---|---|---|
| 3cbg | SAH | O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3cbg | SAH | O-methyltransferase | / | 1.000 | |
| 1sus | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.580 | |
| 3c3y | SAH | O-methyltransferase | / | 0.568 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.566 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.563 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.539 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.531 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.530 | |
| 3a7d | FBN | Catechol O-methyltransferase | 2.1.1.6 | 0.518 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.497 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.496 | |
| 3nw9 | 637 | Catechol O-methyltransferase | 2.1.1.6 | 0.494 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.481 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.473 | |
| 3ozs | OZS | Catechol O-methyltransferase | 2.1.1.6 | 0.472 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.467 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.467 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.466 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.465 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.465 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.463 | |
| 1mdu | ATP | Actin, alpha skeletal muscle | / | 0.458 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.457 | |
| 1sui | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.456 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.456 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.455 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.455 | |
| 3uvp | 048 | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 5br4 | NAD | Lactaldehyde reductase | 1.1.1.77 | 0.455 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2j9m | PY8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.454 | |
| 4jaz | STL | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 4k42 | ADP | Actin, alpha skeletal muscle | / | 0.454 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.453 | |
| 2izr | BRK | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.453 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.453 | |
| 1zq9 | SAM | Probable dimethyladenosine transferase | / | 0.452 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.449 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.448 | |
| 3nwb | 659 | Catechol O-methyltransferase | 2.1.1.6 | 0.448 | |
| 3okf | NAD | 3-dehydroquinate synthase | 4.2.3.4 | 0.448 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.448 | |
| 4cdm | FAD | Deoxyribodipyrimidine photolyase | / | 0.448 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.447 | |
| 2g9u | G27 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.447 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.446 | |
| 1w8c | N69 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 2izs | BRQ | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.445 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.445 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.445 | |
| 4pki | ATP | Actin, alpha skeletal muscle | / | 0.445 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.445 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.445 | |
| 2uyq | SAM | Putative S-adenosyl-L-methionine-dependent methyltransferase ML2640 | 2.1.1 | 0.444 | |
| 3ffk | ATP | Actin, alpha skeletal muscle | / | 0.444 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.443 | |
| 3fz1 | B98 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3uzp | 0CK | Casein kinase I isoform delta | 2.7.11.1 | 0.443 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.443 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.443 | |
| 2b5v | NAP | Glucose 1-dehydrogenase | / | 0.442 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.441 | |
| 2vtp | LZ9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.441 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4hgs | 15G | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.441 | |
| 4s32 | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.441 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.441 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.441 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2ayp | 43A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4a9r | RU5 | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.440 | |
| 4h03 | LAR | Actin, alpha skeletal muscle | / | 0.440 | |
| 4l42 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.440 |