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 |
|---|---|---|---|
| 3tgu | WF3 | Cytochrome b |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3tgu | WF3 | Cytochrome b | / | 1.000 | |
| 3l71 | AZO | Cytochrome b | / | 0.669 | |
| 3l70 | JZV | Cytochrome b | / | 0.609 | |
| 1sqp | MYX | Cytochrome b | / | 0.573 | |
| 1sqb | AZO | Cytochrome b | / | 0.551 | |
| 3h1j | SMA | Cytochrome b | / | 0.504 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.490 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.489 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.488 | |
| 2qjy | SMA | Cytochrome b | / | 0.485 | |
| 1sqq | OST | Cytochrome b | / | 0.483 | |
| 2h42 | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.477 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.474 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.466 | |
| 2e99 | B08 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.465 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.465 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.464 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.463 | |
| 2agv | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.461 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.461 | |
| 3qpn | PFK | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.461 | |
| 3aba | FLI | Cytochrome P450 | / | 0.460 | |
| 2dqs | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.459 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.459 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.458 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.455 | |
| 3p9t | TCL | Repressor | / | 0.455 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.455 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.455 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.454 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.454 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.453 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.453 | |
| 1ddt | APU | Diphtheria toxin | / | 0.452 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.452 | |
| 1kb9 | SMA | Cytochrome b | / | 0.451 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 3nal | DBK | Calcium-transporting ATPase | / | 0.451 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.451 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.450 | |
| 1tw2 | ERT | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.449 | |
| 2ibz | SMA | Cytochrome b | / | 0.449 | |
| 3td8 | D2R | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4xwt | U5P | Ribonuclease J | / | 0.449 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1ek2 | CDU | Bifunctional epoxide hydrolase 2 | / | 0.448 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 3hyw | DCQ | Sulfide-quinone reductase | / | 0.448 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.448 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.448 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.448 | |
| 1ezv | SMA | Cytochrome b | / | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.447 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.447 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.446 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.445 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 4rbs | 0RV | Metallo-beta-lactamase type 2 | / | 0.445 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 2oye | IM8 | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.443 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 2wpw | ACO | Orf14 | / | 0.442 | |
| 3qpp | PFW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2w0b | CMW | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.440 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.440 |