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 |
|---|---|---|---|
| 4uof | DAT | Nucleoside diphosphate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4uof | DAT | Nucleoside diphosphate kinase | / | 1.000 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.678 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.607 | |
| 4fkx | CDP | Nucleoside diphosphate kinase | / | 0.573 | |
| 1zs6 | ADP | Nucleoside diphosphate kinase 3 | 2.7.4.6 | 0.569 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.550 | |
| 3bbf | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.549 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.542 | |
| 1wkl | ATP | Nucleoside diphosphate kinase | / | 0.516 | |
| 2hvd | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.516 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.513 | |
| 2dxe | GDP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.489 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.488 | |
| 2dxf | GNP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.484 | |
| 2dy9 | ADP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.483 | |
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.476 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.475 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.475 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.471 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.467 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.466 | |
| 3up0 | D7S | aceDAF-12 | / | 0.465 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.461 | |
| 5iqa | GNP | Bifunctional AAC/APH | 2.3.1 | 0.461 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.460 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 5iqb | GNP | Bifunctional AAC/APH | 2.3.1 | 0.460 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.459 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.459 | |
| 1lwx | AZD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.458 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.458 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.458 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.456 | |
| 1bux | PPS | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.455 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.453 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.451 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.450 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.450 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.449 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.449 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.447 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.446 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.446 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.445 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.445 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.444 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.443 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.441 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.441 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 2vcx | D26 | Hematopoietic prostaglandin D synthase | / | 0.441 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.441 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3up3 | XCA | aceDAF-12 | / | 0.440 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4die | C5P | Cytidylate kinase | / | 0.440 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.440 | |
| 4g2w | NI0 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 5doz | NDP | JamJ | / | 0.440 |