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 |
|---|---|---|---|
| 3gu3 | SAH | Methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gu3 | SAH | Methyltransferase | / | 1.000 | |
| 4fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.477 | |
| 4fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.477 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.476 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.475 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 4e2y | JHZ | Methyltransferase | / | 0.472 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.469 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.469 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.469 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.468 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.467 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.466 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.466 | |
| 2r8o | T5X | Transketolase 1 | / | 0.466 | |
| 2r8p | T6F | Transketolase 1 | / | 0.466 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.466 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.465 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.465 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.464 | |
| 4qen | SAH | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 | 2.1.1.43 | 0.464 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.463 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.463 | |
| 2r5n | TPP | Transketolase 1 | / | 0.463 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.462 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.462 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.462 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.461 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.460 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.460 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.459 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.459 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.458 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.458 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.458 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.458 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.458 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.456 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.456 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.456 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.455 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.454 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.452 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.452 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.452 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.451 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.451 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.451 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.451 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.451 | |
| 2ejz | SAH | Diphthine synthase | / | 0.450 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 5dp2 | NAP | CurF | / | 0.450 | |
| 2uzf | CAA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.449 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.448 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.448 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.448 | |
| 4xwt | U5P | Ribonuclease J | / | 0.448 | |
| 3hxf | BD9 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.447 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.447 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.446 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.446 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.446 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.446 | |
| 1g7v | PAI | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.445 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.445 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.445 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.444 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.444 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.444 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.444 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.443 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1sa4 | JAN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 4e2z | JHZ | Methyltransferase | / | 0.442 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.441 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 2qe2 | 452 | Polyprotein | / | 0.441 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.441 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.441 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.441 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.440 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.440 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 |