sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 1.000 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.592 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.484 | |
| 5f2k | SAH | Uncharacterized protein | / | 0.484 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.477 | |
| 1e2n | RCA | Thymidine kinase | / | 0.475 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.473 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.473 | |
| 1efa | NPF | Lactose operon repressor | / | 0.472 | |
| 1q4w | DQU | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.472 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.469 | |
| 5epe | SAH | Uncharacterized protein | / | 0.469 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.467 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.465 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.465 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.462 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.458 | |
| 3r8v | Z62 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.458 | |
| 3ll9 | ADP | Isopentenyl phosphate kinase | / | 0.457 | |
| 1vbn | YSA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.455 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.454 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.454 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.453 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.452 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.452 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.452 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.452 | |
| 4giy | 0WY | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.452 | |
| 4yaf | 2AM | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 3nhu | M42 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.451 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.450 | |
| 4fki | 09K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 4e2w | JHZ | Methyltransferase | / | 0.449 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.449 | |
| 1ckp | PVB | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 1daz | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.448 | |
| 2cgv | 3B3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.448 | |
| 3gb4 | D3M | DdmC | / | 0.448 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.448 | |
| 3oxk | 5GP | Histidine triad nucleotide-binding protein | 3 | 0.448 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.448 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.448 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.447 | |
| 3py0 | SU9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.447 | |
| 4ftr | 5HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.446 | |
| 4upj | U04 | Gag-Pol polyprotein | / | 0.445 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.444 | |
| 3rk7 | 08Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3roe | THM | NAD(P)H-hydrate epimerase | 5.1.99.6 | 0.444 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.444 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.443 | |
| 4gqi | M49 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.443 | |
| 1n06 | ADP | Riboflavin kinase | 2.7.1.26 | 0.442 | |
| 1pxl | CK4 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.442 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.442 | |
| 4rtp | SAM | DNA adenine methylase | 2.1.1.72 | 0.442 | |
| 4zvm | DM2 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.442 | |
| 2bif | ANP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.441 | |
| 2e9v | 85A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2r4t | ADP | Glycogen synthase | 2.4.1.21 | 0.441 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4e31 | JHZ | Methyltransferase | / | 0.441 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.440 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.440 | |
| 2xmy | CDK | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 | |
| 5iqe | GNP | Bifunctional AAC/APH | 2.3.1 | 0.440 |