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 |
|---|---|---|---|
| 3ipt | EQU | Steroid Delta-isomerase | 5.3.3.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ipt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 1.000 | |
| 1e3r | AND | Steroid Delta-isomerase | 5.3.3.1 | 0.542 | |
| 1e3v | DXC | Steroid Delta-isomerase | 5.3.3.1 | 0.520 | |
| 3fzw | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.519 | |
| 1cqs | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.511 | |
| 1ogx | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.507 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.496 | |
| 1gs3 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.493 | |
| 4h4o | 506 | Gag-Pol polyprotein | 2.7.7.49 | 0.491 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.488 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.485 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.484 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.483 | |
| 2zym | ACX | Periplasmic binding protein | / | 0.481 | |
| 3ows | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.479 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.475 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.474 | |
| 1brp | RTL | Retinol-binding protein 4 | / | 0.471 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 3owu | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.471 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 4qa1 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.470 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.469 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 3ezp | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.466 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.465 | |
| 1oho | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.465 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.465 | |
| 3owy | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.465 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.465 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.464 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.463 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.463 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.462 | |
| 4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.462 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.461 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.460 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.460 | |
| 5dc5 | B3N | Histone deacetylase 8 | 3.5.1.98 | 0.460 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.459 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.458 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.458 | |
| 1aqb | RTL | Retinol-binding protein 4 | / | 0.457 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.457 | |
| 1e7a | PFL | Serum albumin | / | 0.456 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.455 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.454 | |
| 2zyn | BCD | Periplasmic binding protein | / | 0.454 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.453 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.453 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.450 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.450 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.450 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.449 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.449 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.449 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.448 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.448 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.448 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.447 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.447 | |
| 1w22 | NHB | Histone deacetylase 8 | 3.5.1.98 | 0.447 | |
| 2ilu | NDP | Lactaldehyde dehydrogenase | 1.2.1.22 | 0.447 | |
| 3h1j | SMA | Cytochrome b | / | 0.447 | |
| 4iah | 1DX | Alr2278 protein | / | 0.447 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.447 | |
| 4k5y | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.447 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.446 | |
| 3acw | 651 | Dehydrosqualene synthase | / | 0.446 | |
| 3nax | MP7 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.446 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.445 | |
| 3o9l | LPN | Renin | 3.4.23.15 | 0.445 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.444 | |
| 1iiu | RTL | Retinol-binding protein 4 | / | 0.444 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.444 | |
| 3tfq | 07M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.444 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 1khr | COA | Streptogramin A acetyltransferase | 2.3.1 | 0.443 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.443 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.443 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1sqv | UHD | Cytochrome b | / | 0.442 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.442 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 4af3 | VX6 | Aurora kinase B | 2.7.11.1 | 0.441 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.441 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.441 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.440 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.440 | |
| 2vqo | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.440 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.440 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.440 | |
| 4ea1 | 3RX | Dehydrosqualene synthase | / | 0.440 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.440 |