sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3c10 | TSN | Histone deacetylase 7 | 3.5.1.98 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3c10 | TSN | Histone deacetylase 7 | 3.5.1.98 | 1.000 | |
| 3zns | NU7 | Histone deacetylase 7 | 3.5.1.98 | 0.570 | |
| 3znr | NU9 | Histone deacetylase 7 | 3.5.1.98 | 0.557 | |
| 4cby | KEE | Histone deacetylase 4 | 3.5.1.98 | 0.551 | |
| 3c0z | SHH | Histone deacetylase 7 | 3.5.1.98 | 0.539 | |
| 1e92 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.510 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.499 | |
| 2vqj | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.498 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.492 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.491 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.488 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.485 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.483 | |
| 4a4l | 939 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.481 | |
| 2xnp | WCX | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.480 | |
| 2qhx | FE1 | Pteridine reductase 1 | 1.5.1.33 | 0.477 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.477 | |
| 5bvw | 1N1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.474 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.473 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.473 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.473 | |
| 2w5b | AGS | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.473 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.472 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.472 | |
| 2ilu | NDP | Lactaldehyde dehydrogenase | 1.2.1.22 | 0.472 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.471 | |
| 2xnn | 430 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.470 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.469 | |
| 3ele | PLP | Aminotransferase | / | 0.469 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.468 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.467 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.467 | |
| 2gfs | PQB | Mitogen-activated protein kinase 14 | / | 0.466 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.464 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.462 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.462 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.462 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.462 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.462 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.461 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.461 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2hp2 | KE4 | Glutamate-1-semialdehyde 2,1-aminomutase | 5.4.3.8 | 0.459 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.459 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.459 | |
| 1e7w | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.458 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.458 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.458 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.458 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4afe | GGY | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.458 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 1g3m | PCQ | Estrogen sulfotransferase | 2.8.2.4 | 0.457 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 3nxy | D2H | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.456 | |
| 3pn1 | IVH | DNA ligase | / | 0.456 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.456 | |
| 4b6l | 9ZP | Serine/threonine-protein kinase PLK3 | 2.7.11.21 | 0.456 | |
| 2acw | UPG | Glycosyltransferase | / | 0.455 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 4qx5 | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.455 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.455 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.454 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.454 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.453 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.453 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 4c2p | X8Z | Angiotensin-converting enzyme | 3.2.1 | 0.453 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.452 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.451 | |
| 1wkh | PPE | [LysW]-aminoadipate semialdehyde transaminase | / | 0.451 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.451 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.451 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.451 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.451 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.451 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.450 | |
| 1m8h | 6NI | Nitric oxide synthase, inducible | 1.14.13.39 | 0.450 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.449 | |
| 1vgr | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.449 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4jqa | ID8 | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1odj | GMP | Purine nucleoside phosphorylase | / | 0.448 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 3jq8 | DX3 | Pteridine reductase, putative | / | 0.448 | |
| 4mm7 | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.448 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.448 | |
| 1fxf | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 3bld | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 4bqu | CLR | Japanin | / | 0.447 | |
| 4hsh | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.447 | |
| 1xmm | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.446 | |
| 2o98 | FSC | 14-3-3-like protein C | / | 0.446 | |
| 2pbz | ATP | Uncharacterized protein | / | 0.446 | |
| 4blc | NDP | Catalase | 1.11.1.6 | 0.446 | |
| 4boe | CLR | Japanin | / | 0.446 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.446 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.445 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.445 | |
| 3g5m | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.445 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1w19 | T4P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.444 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.444 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.444 | |
| 2y67 | N21 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.444 | |
| 2zxg | S23 | Aminopeptidase N | 3.4.11.2 | 0.444 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.444 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.444 | |
| 4i0t | 1B6 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.444 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.443 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.443 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.443 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.443 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.443 | |
| 1i05 | LTL | Major urinary protein 6 | / | 0.442 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.442 | |
| 2jav | 5Z5 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.442 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.442 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.442 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 2xnm | WGZ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.441 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.441 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.441 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.441 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4n65 | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.441 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.440 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2wqo | VGK | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.440 | |
| 3ba6 | AN2 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.440 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3nhf | VVV | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.440 |