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 |
|---|---|---|---|
| 1h5t | TYD | Glucose-1-phosphate thymidylyltransferase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1h5t | TYD | Glucose-1-phosphate thymidylyltransferase 1 | / | 1.000 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.588 | |
| 5ify | UMP | Glucose-1-phosphate thymidylyltransferase | / | 0.580 | |
| 4ho4 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.549 | |
| 4asy | N5Y | Glucose-1-phosphate thymidylyltransferase | / | 0.548 | |
| 1g0r | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.540 | |
| 1fxo | TMP | Glucose-1-phosphate thymidylyltransferase | / | 0.531 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.523 | |
| 4ho9 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.506 | |
| 1g4p | FQP | Thiamine-phosphate synthase | / | 0.496 | |
| 4b42 | 942 | Glucose-1-phosphate thymidylyltransferase | / | 0.491 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.487 | |
| 1g6c | IFP | Thiamine-phosphate synthase | / | 0.477 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.476 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.474 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.474 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.472 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.470 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.469 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.468 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 4asj | N6A | Glucose-1-phosphate thymidylyltransferase | / | 0.467 | |
| 4b2w | BZ0 | Glucose-1-phosphate thymidylyltransferase | / | 0.467 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.466 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.465 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.464 | |
| 1g6c | TZP | Thiamine-phosphate synthase | / | 0.463 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.463 | |
| 1mdu | ATP | Actin, alpha skeletal muscle | / | 0.462 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.462 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.462 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 1g69 | TZP | Thiamine-phosphate synthase | / | 0.461 | |
| 1eyq | NAR | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.459 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.459 | |
| 2o3u | NGD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.459 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.459 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.457 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.457 | |
| 3o15 | IFP | Thiamine-phosphate synthase | / | 0.457 | |
| 4b5b | BBE | Glucose-1-phosphate thymidylyltransferase | / | 0.456 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.455 | |
| 2ay3 | MPP | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.455 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.455 | |
| 5fkm | TDC | Tetracycline repressor protein class D | / | 0.455 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.454 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.454 | |
| 3ef5 | DGT | Probable pyrophosphohydrolase | / | 0.454 | |
| 1f28 | UMP | Thymidylate synthase | 2.1.1.45 | 0.453 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.453 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.453 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4xb2 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.453 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.452 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.452 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.452 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.452 | |
| 1g67 | TZP | Thiamine-phosphate synthase | / | 0.451 | |
| 1pxx | DIF | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.451 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.451 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.451 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.451 | |
| 4b4b | GJB | Glucose-1-phosphate thymidylyltransferase | / | 0.451 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.450 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.450 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.450 | |
| 4dij | BLF | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.450 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.450 | |
| 4xiv | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.450 | |
| 1dj3 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.449 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.449 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.449 | |
| 2xrl | DXT | Tetracycline repressor protein class D | / | 0.449 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.449 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 1u5r | ATP | Serine/threonine-protein kinase TAO2 | 2.7.11.1 | 0.448 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 3uvp | 048 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.447 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2ay9 | 5PV | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.447 | |
| 2fto | TMP | Thymidylate synthase | / | 0.446 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.446 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.446 | |
| 3r34 | COA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.446 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4n9w | GDP | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.446 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.446 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.445 | |
| 1l7e | NAI | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.445 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.444 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.444 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.444 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4la0 | 198 | Serum albumin | / | 0.444 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.444 | |
| 1q97 | ATP | Serine/threonine-protein kinase SKY1 | 2.7.11.1 | 0.443 | |
| 2xvv | 9DN | Serum albumin | / | 0.443 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.443 | |
| 4b4g | KKT | Glucose-1-phosphate thymidylyltransferase | / | 0.443 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.443 | |
| 4kp5 | E1F | Carbonic anhydrase 12 | 4.2.1.1 | 0.443 | |
| 4ysw | FAD | Xanthine dehydrogenase/oxidase | / | 0.443 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.442 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.442 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.442 | |
| 3m9v | TYD | FAD-dependent oxidoreductase | / | 0.442 | |
| 3wow | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.442 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.441 | |
| 1pl8 | NAD | Sorbitol dehydrogenase | 1.1.1.14 | 0.441 | |
| 2ay8 | 4TB | Aromatic-amino-acid aminotransferase | 2.6.1.57 | 0.441 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.441 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.441 | |
| 3lj3 | WYE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 3r35 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.441 | |
| 3zux | TCH | Transporter | / | 0.441 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.441 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.441 | |
| 4otp | ADP | Serine/threonine-protein kinase RIO1 | 2.7.11.1 | 0.441 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
| 1sez | OMN | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.440 | |
| 1sn0 | T44 | Transthyretin | / | 0.440 | |
| 2bdf | 24A | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.440 | |
| 2xgo | ZKD | Uncharacterized protein | / | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.440 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.440 | |
| 4p6w | MOF | Glucocorticoid receptor | / | 0.440 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.440 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.440 |