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 |
|---|---|---|---|
| 4uof | DAT | Nucleoside diphosphate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4uof | DAT | Nucleoside diphosphate kinase | / | 1.000 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.685 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.616 | |
| 4fkx | CDP | Nucleoside diphosphate kinase | / | 0.573 | |
| 1zs6 | ADP | Nucleoside diphosphate kinase 3 | 2.7.4.6 | 0.572 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.555 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.552 | |
| 3bbf | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.550 | |
| 2hvd | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.526 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.519 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.517 | |
| 1wkl | ATP | Nucleoside diphosphate kinase | / | 0.516 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.491 | |
| 2dxe | GDP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.489 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.488 | |
| 2dxf | GNP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.484 | |
| 2dy9 | ADP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.483 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.479 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.477 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.477 | |
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.475 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.475 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.468 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.467 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.467 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3up0 | D7S | aceDAF-12 | / | 0.465 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.462 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.461 | |
| 5iqa | GNP | Bifunctional AAC/APH | 2.3.1 | 0.461 | |
| 1bux | PPS | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.460 | |
| 5iqb | GNP | Bifunctional AAC/APH | 2.3.1 | 0.460 | |
| 1lwx | AZD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.459 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.459 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.459 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.459 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.459 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.458 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.458 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.455 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.453 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.452 | |
| 5doz | NDP | JamJ | / | 0.452 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.451 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.451 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.450 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.450 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 2x0e | TYD | WsaF | / | 0.449 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.447 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.447 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.446 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.446 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.446 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.445 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.445 | |
| 4die | C5P | Cytidylate kinase | / | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1cbs | REA | Cellular retinoic acid-binding protein 2 | / | 0.444 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.444 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 5ej5 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.444 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.443 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.443 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.443 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.443 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.443 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.442 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.442 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 3gep | 24H | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.442 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4bva | T3 | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4kf1 | HT5 | Aryldialkylphosphatase | 3.1.8.1 | 0.441 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.440 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3up3 | XCA | aceDAF-12 | / | 0.440 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.440 |