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 |
|---|---|---|---|
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.786 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.669 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.652 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.647 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.624 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.587 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.524 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.474 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.470 | |
| 2ejz | SAH | Diphthine synthase | / | 0.470 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 3e6e | DCS | Alanine racemase | / | 0.467 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.461 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.461 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.460 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.460 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.458 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.457 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.456 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1ahg | TYR_PLP | Aspartate aminotransferase | 2.6.1.1 | 0.455 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.455 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.455 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.453 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.452 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.452 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.450 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.450 | |
| 4j7g | TRH | PCZA361.3 | / | 0.450 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.450 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.449 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.448 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.447 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.447 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.446 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.446 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.446 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.445 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.445 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.445 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.445 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 3klb | FMN | Uncharacterized protein | / | 0.444 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.444 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.443 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.443 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.443 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.443 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.442 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.441 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.440 | |
| 1vfs | DCS | Alanine racemase | / | 0.440 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.440 |