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 |
|---|---|---|---|
| 4jhi | EMU | Nodulin-13 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4jhi | EMU | Nodulin-13 | / | 1.000 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.494 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.482 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.478 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.476 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.476 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.476 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.468 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.464 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.464 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.463 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.461 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.461 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.460 | |
| 1xj7 | DHT | Androgen receptor | / | 0.460 | |
| 2w71 | L23 | Biotin carboxylase | 6.3.4.14 | 0.460 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 1fml | RTL | Retinol dehydratase | / | 0.458 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2pio | DHT | Androgen receptor | / | 0.457 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.457 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.457 | |
| 1gs4 | ZK5 | Androgen receptor | / | 0.456 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.456 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 2piw | DHT | Androgen receptor | / | 0.453 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.453 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 1c7o | PPG | Hemolysin | / | 0.452 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.452 | |
| 4muw | 2F4 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.451 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.450 | |
| 4m6l | 21V | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.449 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.447 | |
| 1ry8 | RUT | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 4jnc | 1LF | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.447 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.444 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.444 | |
| 3uf7 | ASP_ILE_PRO_PHE | Uracil-DNA glycosylase | 3.2.2.27 | 0.444 | |
| 4iah | 1DX | Alr2278 protein | / | 0.444 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.443 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3lnb | COA | N-acetyltransferase family protein | / | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1m9j | CLW | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.442 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 2pit | DHT | Androgen receptor | / | 0.441 | |
| 2piv | DHT | Androgen receptor | / | 0.441 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.441 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.440 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2ama | DHT | Androgen receptor | / | 0.440 | |
| 2xvw | 9NR | Serum albumin | / | 0.440 | |
| 2ylq | TES | Androgen receptor | / | 0.440 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.440 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.440 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.440 |