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 |
|---|---|---|---|
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 1.000 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.691 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.571 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.491 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.489 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.478 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.476 | |
| 2xvv | 9DN | Serum albumin | / | 0.476 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.474 | |
| 3b9l | AZZ | Serum albumin | / | 0.473 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.472 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.470 | |
| 2wi7 | 2KL | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.468 | |
| 3qly | 55V | Uncharacterized protein | / | 0.468 | |
| 4u7w | NDP | MxaA | / | 0.468 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.467 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 2xvw | 9NR | Serum albumin | / | 0.466 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.464 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.462 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.461 | |
| 1r2j | FAD | FkbI | / | 0.461 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.461 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.461 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3ceh | AVE | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.460 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.460 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.457 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.457 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.456 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.456 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.455 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.455 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2bxq | IMN | Serum albumin | / | 0.454 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.453 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.451 | |
| 2bxo | OPB | Serum albumin | / | 0.450 | |
| 3v2u | ATP | Protein GAL3 | / | 0.450 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.449 | |
| 2ati | IHU | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.449 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.448 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.448 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.448 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.448 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1dv2 | ATP | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.447 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.447 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4zwg | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.447 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.446 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.446 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 2e08 | SAH | Diphthine synthase | / | 0.446 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4e0i | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.446 | |
| 4mq1 | 2C3 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 2.7.12.1 | 0.446 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.446 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.446 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.445 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.445 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.444 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 2wpx | ACO | Orf14 | / | 0.444 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.444 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4b1f | KRH | Glutamate racemase | / | 0.444 | |
| 4bgg | 844 | Activin receptor type-1 | 2.7.11.30 | 0.444 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.444 | |
| 1d2s | DHT | Sex hormone-binding globulin | / | 0.443 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.443 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.443 | |
| 1g28 | FMN | PHY3 | / | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.442 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.441 | |
| 3qf9 | NM8 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.441 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.441 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2vo4 | GTB | 2,4-D inducible glutathione S-transferase | / | 0.440 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.440 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.440 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.440 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.440 |