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 |
|---|---|---|---|
| 2opb | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2opb | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 1.000 | |
| 2ony | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.710 | |
| 2onz | TMJ | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.687 | |
| 2g8n | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.630 | |
| 2obf | F83 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.615 | |
| 2g72 | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.527 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.481 | |
| 4fc0 | 0T2 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.469 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.468 | |
| 3w8z | HTK | Putative FAD-dependent oxygenase EncM | / | 0.467 | |
| 3pn1 | IVH | DNA ligase | / | 0.464 | |
| 1it7 | GUN | tRNA-guanine(15) transglycosylase | 2.4.2.48 | 0.463 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.463 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.460 | |
| 2jj1 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.460 | |
| 2jj1 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.460 | |
| 2yat | EEU | Estrogen receptor | / | 0.460 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.460 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.460 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.459 | |
| 2jj2 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.458 | |
| 2jj2 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.458 | |
| 3dej | RXC | Caspase-3 | 3.4.22.56 | 0.457 | |
| 4d2d | ALA_ALA_ALA | Di-or tripeptide:H+ symporter | / | 0.456 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.454 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.454 | |
| 1s2g | 3D1 | Nucleoside 2-deoxyribosyltransferase | / | 0.454 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.454 | |
| 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 | 0.453 | |
| 3s41 | S41 | Glucokinase | 2.7.1.2 | 0.453 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 2d06 | EST | Sulfotransferase 1A1 | 2.8.2.1 | 0.452 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3qp8 | HL0 | Transcriptional activator, LuxR/UhpA family of regulators | / | 0.452 | |
| 3fkn | FKN | Mitogen-activated protein kinase 14 | / | 0.451 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.450 | |
| 3p9t | TCL | Repressor | / | 0.450 | |
| 4hni | 16W | Casein kinase I isoform epsilon | 2.7.11.1 | 0.450 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.450 | |
| 1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.449 | |
| 4buf | F36 | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 4h1j | 0YH | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.448 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 1kf6 | HQO | Fumarate reductase iron-sulfur subunit | 1.3.5.1 | 0.447 | |
| 1kf6 | HQO | Fumarate reductase subunit C | / | 0.447 | |
| 1kf6 | HQO | Fumarate reductase subunit D | / | 0.447 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.447 | |
| 2x9v | TMQ | Pteridine reductase | / | 0.446 | |
| 3ean | NAP | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.446 | |
| 3lm4 | HPX | Catechol 2,3-dioxygenase | / | 0.446 | |
| 4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.446 | |
| 1s9d | AFB | Cytohesin-2 | / | 0.445 | |
| 1s9d | AFB | ADP-ribosylation factor 1 | / | 0.445 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3o73 | O73 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4ea2 | RWZ | Dehydrosqualene synthase | / | 0.445 | |
| 1pf7 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.444 | |
| 3lla | ACP | Myosin heavy chain kinase A | 2.7.11.7 | 0.444 | |
| 3rhj | NAP | Cytosolic 10-formyltetrahydrofolate dehydrogenase | 1.5.1.6 | 0.443 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.443 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.442 | |
| 3ikt | NAD | Redox-sensing transcriptional repressor Rex | / | 0.442 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.442 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 4ddr | MMV | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.442 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 1p72 | THM | Thymidine kinase | / | 0.441 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.441 | |
| 3d2d | REN | Reticuline oxidase | 1.21.3.3 | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
| 4li8 | 1XQ | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 |