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 |
|---|---|---|---|
| 3aos | JH2 | Hemolymph juvenile hormone binding protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 1.000 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.512 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.502 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.501 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.494 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.491 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.491 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.484 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.483 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.477 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.476 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.476 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 4e2y | JHZ | Methyltransferase | / | 0.473 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.472 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.470 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 1r2j | FAD | FkbI | / | 0.467 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3eku | CY9 | Actin-5C | / | 0.464 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.463 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.463 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 1fml | RTL | Retinol dehydratase | / | 0.460 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.460 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.460 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.460 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.459 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.457 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.457 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.457 | |
| 1dtp | APU | Diphtheria toxin | / | 0.456 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.456 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.456 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.455 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.452 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.451 | |
| 3c1o | NAP | Eugenol synthase | / | 0.451 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.450 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.450 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.449 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.448 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4o7u | THF | Thymidylate synthase | / | 0.448 | |
| 1eio | GCH | Gastrotropin | / | 0.447 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.447 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2b03 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.446 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.445 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.445 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.444 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.444 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.443 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.442 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 1uh5 | TCL | Enoyl-ACP reductase | / | 0.442 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.442 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.441 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.441 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.440 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.440 |