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 |
|---|---|---|---|
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 1.000 | |
| 3dej | RXC | Caspase-3 | 3.4.22.56 | 0.494 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.488 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.479 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.477 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.473 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.471 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.468 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 2v34 | CTN | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.465 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.463 | |
| 1nv8 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.463 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.463 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.462 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.462 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.461 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.461 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.461 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.459 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.458 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.457 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.457 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.457 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.456 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.455 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.455 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.454 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.454 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 1svg | I04 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.450 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.449 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.449 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.449 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.448 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.448 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.448 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.448 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.448 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.447 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.447 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.447 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.446 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.445 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.445 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.444 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.444 | |
| 3dnd | LL2 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.444 | |
| 1bzl | FAD | Trypanothione reductase | 1.8.1.12 | 0.443 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.443 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.443 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.442 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2bxm | IMN | Serum albumin | / | 0.442 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 2zif | SAM | Methyltransferase | / | 0.442 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4elb | 34S | Dihydrofolate reductase | / | 0.442 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.441 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.441 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.440 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.440 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.440 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.440 |