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 |
|---|---|---|---|
| 3m6l | TPP | Transketolase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3m6l | TPP | Transketolase | / | 1.000 | |
| 3m34 | TPP | Transketolase | / | 0.590 | |
| 3m7i | TPP | Transketolase | / | 0.543 | |
| 4c7x | TPP | Transketolase | / | 0.522 | |
| 3upt | TPP | Transketolase | / | 0.476 | |
| 3b82 | NAD | Exotoxin A | 2.4.2.36 | 0.475 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.468 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.467 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.466 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.465 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.465 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.463 | |
| 5dw5 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.463 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.462 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.461 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.459 | |
| 2yj4 | ATP | Copper-transporting ATPase | / | 0.458 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.458 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.456 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.456 | |
| 2opb | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.455 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.454 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.454 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.454 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.453 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.453 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.453 | |
| 2nm2 | NEU | Dihydroneopterin aldolase | / | 0.451 | |
| 1n5v | NOM | ActVA 6 protein | / | 0.450 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.450 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.450 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.449 | |
| 1fml | RTL | Retinol dehydratase | / | 0.449 | |
| 3smk | CW7 | 14-3-3 protein sigma | / | 0.449 | |
| 4std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.448 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.448 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.448 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.448 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.448 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.447 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.447 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.447 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.446 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 2w02 | ATP | AcsD | / | 0.446 | |
| 3iog | SDF | Metallo-beta-lactamase type 2 | / | 0.446 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.446 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 2e20 | B4P | Propionate kinase | / | 0.445 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3w5u | FAD | Ferredoxin | / | 0.445 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.444 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.444 | |
| 5c4n | NAP | Precorrin-6A reductase | 1.3.1.54 | 0.444 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.443 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.443 | |
| 2gtb | AZP | Orf1ab polyprotein | / | 0.443 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.443 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.443 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.443 | |
| 4h7z | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.443 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 1dmy | AZM | Carbonic anhydrase 5A, mitochondrial | 4.2.1.1 | 0.442 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.442 | |
| 4oma | LCS | Methionine gamma-lyase | / | 0.442 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.442 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.441 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 2vxk | COA | Glucosamine 6-phosphate acetyltransferase, putative | / | 0.440 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 4f0e | 0RU | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.440 |