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 |
|---|---|---|---|
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 1.000 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.686 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.675 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.664 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.627 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.620 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.612 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.596 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.578 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.551 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.508 | |
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 0.504 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.494 | |
| 2zsc | BTN | Tamavidin2 | / | 0.488 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.479 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.478 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.477 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.476 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.475 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.475 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.475 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.474 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.474 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.473 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.471 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.467 | |
| 1lke | DOG | Bilin-binding protein | / | 0.466 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.466 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.465 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.464 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.464 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.464 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.462 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.462 | |
| 1g28 | FMN | PHY3 | / | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.460 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.460 | |
| 4blw | SAH | Ribosomal RNA large subunit methyltransferase J | / | 0.460 | |
| 1p4m | ADP | Riboflavin kinase | 2.7.1.26 | 0.459 | |
| 3up0 | D7S | aceDAF-12 | / | 0.459 | |
| 4e2x | SAH | Methyltransferase | / | 0.459 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.458 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.457 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.457 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.457 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.456 | |
| 4y1b | NAP | AntE | / | 0.455 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.454 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.454 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.454 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.454 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.453 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.453 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.453 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.453 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.452 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.452 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.452 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.451 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.451 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.451 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.451 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.451 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.450 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 2xlt | NA0 | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.450 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.450 | |
| 3r96 | ACO | MccE protein | / | 0.450 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.450 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.450 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.449 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.449 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.448 | |
| 3gxo | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.448 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.447 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.447 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.447 | |
| 2xvh | NAP | Putative flavin-containing monooxygenase | / | 0.447 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.447 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.447 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.446 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.446 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.446 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.446 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3tp0 | FO5 | HTH-type transcriptional regulator EthR | / | 0.446 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.446 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.446 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.446 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.445 | |
| 3up3 | XCA | aceDAF-12 | / | 0.445 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.445 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.444 | |
| 2q0g | UPU | Poly(A) polymerase, putative | / | 0.444 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.444 | |
| 3axs | SFG | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.444 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.444 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1swn | BTN | Streptavidin | / | 0.443 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.443 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.443 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.443 | |
| 4rv9 | SAH | D-mycarose 3-C-methyltransferase | / | 0.443 | |
| 5epe | SAH | Uncharacterized protein | / | 0.443 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 1pg3 | PRX | Acetyl-coenzyme A synthetase | / | 0.441 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.441 | |
| 4ax8 | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.441 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.441 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.440 | |
| 1n4q | LYS_CYS_VAL_ILE_LEU | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.440 | |
| 3klb | FMN | Uncharacterized protein | / | 0.440 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.440 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4j7h | TRH | PCZA361.3 | / | 0.440 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.440 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.440 |