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 |
|---|---|---|---|
| 2vcg | S17 | Histone deacetylase-like amidohydrolase | 3.5.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vcg | S17 | Histone deacetylase-like amidohydrolase | 3.5.1 | 1.000 | |
| 2gh6 | CF3 | Histone deacetylase-like amidohydrolase | 3.5.1 | 0.604 | |
| 1zz1 | SHH | Histone deacetylase-like amidohydrolase | 3.5.1 | 0.557 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.498 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.489 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.482 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.481 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.479 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.479 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.477 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.476 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.472 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.471 | |
| 1k9s | FM2 | Purine nucleoside phosphorylase DeoD-type | / | 0.470 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.470 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.469 | |
| 4zas | TYD | CalS13 | / | 0.468 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.467 | |
| 3cth | 319 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.466 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 3vjc | ZGA | Squalene synthase | 2.5.1.21 | 0.466 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.465 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.464 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.463 | |
| 4dbu | BT9 | Aldo-keto reductase family 1 member C3 | / | 0.463 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.463 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.462 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 4bfp | SWY | Tankyrase-2 | 2.4.2.30 | 0.461 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 4ky4 | 04J | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.461 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.460 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.459 | |
| 3fu8 | 3DM | Laccase-1 | 1.10.3.2 | 0.459 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.459 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.458 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 4iae | 1DX | Alr2278 protein | / | 0.458 | |
| 2bxo | OPB | Serum albumin | / | 0.457 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.457 | |
| 4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.457 | |
| 4hni | 16W | Casein kinase I isoform epsilon | 2.7.11.1 | 0.455 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.454 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.453 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.453 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.453 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.452 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.452 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4myq | 19T | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 4rw4 | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.451 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.450 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.449 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3jsu | KA5 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.446 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.446 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.446 | |
| 3up3 | XCA | aceDAF-12 | / | 0.446 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 1e1f | PSG | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.445 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 1sqq | OST | Cytochrome b | / | 0.445 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.445 | |
| 4dm6 | TTB | Retinoic acid receptor beta | / | 0.445 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.445 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2p15 | EZT | Estrogen receptor | / | 0.444 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 4ea2 | RWZ | Dehydrosqualene synthase | / | 0.444 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.443 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.443 | |
| 4htx | 19F | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.443 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.442 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.442 | |
| 4h38 | 0YX | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3o8g | O8G | HTH-type transcriptional regulator EthR | / | 0.441 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 1zdw | FLV | Prenyltransferase | / | 0.440 | |
| 2b5j | 3AC | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 3fu9 | KIB | Laccase-1 | 1.10.3.2 | 0.440 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.440 |