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 |
|---|---|---|---|
| 1lmc | BUL | Lysozyme C II | 3.2.1.17 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1lmc | BUL | Lysozyme C II | 3.2.1.17 | 1.000 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.504 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.487 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.479 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 2pcg | SAH | Diphthine synthase | / | 0.475 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 2emu | SAH | Diphthine synthase | / | 0.472 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.471 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.470 | |
| 2iml | FMN | Uncharacterized protein | / | 0.470 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.469 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 2huv | SAH | Diphthine synthase | / | 0.468 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.468 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.468 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.467 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.465 | |
| 2pca | SAH | Diphthine synthase | / | 0.465 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.465 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.465 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.464 | |
| 3t6i | NC9 | Endothiapepsin | 3.4.23.22 | 0.464 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.463 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.463 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4mfe | BTN | Pyruvate carboxylase | / | 0.463 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.462 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.462 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.461 | |
| 2egb | SAH | Diphthine synthase | / | 0.460 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.460 | |
| 3a20 | FMN | FMN-binding protein | / | 0.460 | |
| 3qbw | ADP | Anhydro-N-acetylmuramic acid kinase | / | 0.460 | |
| 1g8o | U5P | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.459 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.459 | |
| 4pkw | GM6 | Lethal factor | 3.4.24.83 | 0.459 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.458 | |
| 2egs | SAH | Diphthine synthase | / | 0.458 | |
| 2e7r | SAH | Diphthine synthase | / | 0.457 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.457 | |
| 3t6i | NC8 | Endothiapepsin | 3.4.23.22 | 0.457 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.457 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.456 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.456 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.456 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.456 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.455 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.455 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.455 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.455 | |
| 2e4n | SAH | Diphthine synthase | / | 0.454 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1til | ATP | Anti-sigma F factor | / | 0.453 | |
| 2ehl | SAH | Diphthine synthase | / | 0.453 | |
| 2pck | SAH | Diphthine synthase | / | 0.453 | |
| 5ans | RX8 | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.453 | |
| 2eld | SAH | Diphthine synthase | / | 0.452 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.452 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.452 | |
| 1gaw | FAD | Ferredoxin | / | 0.451 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.451 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.451 | |
| 1owm | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.450 | |
| 2p9d | SAH | Diphthine synthase | / | 0.450 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.450 | |
| 2wgj | VGH | Hepatocyte growth factor receptor | 2.7.10.1 | 0.450 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.450 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.449 | |
| 2zre | AGS | Protein RecA | / | 0.449 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.449 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.449 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.448 | |
| 2el3 | SAH | Diphthine synthase | / | 0.448 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.448 | |
| 2jj8 | AZZ | Deoxynucleoside kinase | / | 0.447 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2vk8 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.446 | |
| 1b3r | NAD | Adenosylhomocysteinase | 3.3.1.1 | 0.445 | |
| 2e15 | SAH | Diphthine synthase | / | 0.445 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.445 | |
| 3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4c35 | NU3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 1g9r | UPF | LgtC | / | 0.444 | |
| 2dsg | SAH | Diphthine synthase | / | 0.444 | |
| 2nr4 | FMN | Conserved protein | / | 0.444 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.444 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.444 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.443 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.443 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.443 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.443 | |
| 2p6l | SAH | Diphthine synthase | / | 0.443 | |
| 2pch | SAH | Diphthine synthase | / | 0.443 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.443 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.443 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.443 | |
| 5bn4 | ANP | V-type ATP synthase alpha chain | / | 0.443 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 2p6d | SAH | Diphthine synthase | / | 0.442 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.442 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.442 | |
| 2dxx | SAH | Diphthine synthase | / | 0.441 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.441 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3lth | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.441 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 1own | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 1ppj | ANY | Cytochrome b | / | 0.440 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.440 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.440 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.440 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.440 | |
| 3tg4 | SAM | N-lysine methyltransferase SMYD2 | / | 0.440 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |