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 |
|---|---|---|---|
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 1.000 | |
| 1af7 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.534 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.495 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.494 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.487 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.478 | |
| 3eey | SAM | rRNA methylase | / | 0.471 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.471 | |
| 1izh | Q50 | Protease | / | 0.467 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.466 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.465 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 5dp2 | NAP | CurF | / | 0.461 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.460 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.460 | |
| 3lbf | SAH | Protein-L-isoaspartate O-methyltransferase | 2.1.1.77 | 0.459 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.459 | |
| 5je4 | SAH | Methyl transferase | / | 0.459 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.458 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.457 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.456 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.455 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.455 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.454 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.453 | |
| 1d4h | BEH | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.453 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.453 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.453 | |
| 3nu6 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.451 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.451 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.451 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.451 | |
| 2r5p | MK1 | Gag-Pol polyprotein | / | 0.450 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.450 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.449 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.449 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.448 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1py5 | PY1 | TGF-beta receptor type-1 | 2.7.11.30 | 0.447 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.447 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.447 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.446 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.446 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.445 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.445 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.445 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4yaf | 2AM | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1idb | 0DO | Gag-Pol polyprotein | / | 0.444 | |
| 1mew | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.444 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.444 | |
| 3o9e | A60 | Pol polyprotein | / | 0.444 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.443 | |
| 4j54 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4zvm | DM2 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.443 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.442 | |
| 2r8p | T6F | Transketolase 1 | / | 0.442 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 4h3z | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.442 | |
| 5epe | SAH | Uncharacterized protein | / | 0.442 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.441 | |
| 3gb4 | D3M | DdmC | / | 0.441 | |
| 3wsj | MK1 | Protease | / | 0.441 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.441 | |
| 1mtr | PI6 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.440 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.440 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.440 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.440 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.440 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.440 |