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 |
|---|---|---|---|
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 1.000 | |
| 4ock | ANP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.717 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.617 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.613 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.567 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.478 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.474 | |
| 3nw3 | MU2 | Peptidoglycan recognition protein 1 | / | 0.473 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.473 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.472 | |
| 1hzj | UD1 | UDP-glucose 4-epimerase | / | 0.471 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.469 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.469 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.469 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.466 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.465 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.465 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.464 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.463 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.463 | |
| 4fgr | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 6.3.2.6 | 0.463 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.462 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.462 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.461 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.461 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.461 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.460 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.460 | |
| 5dp2 | NAP | CurF | / | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.459 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.458 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.458 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.458 | |
| 3nbv | ANP | Ketohexokinase | / | 0.457 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.456 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.456 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.456 | |
| 4xwt | U5P | Ribonuclease J | / | 0.456 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.455 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.455 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.455 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.454 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.454 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.453 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.453 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.453 | |
| 4kto | FAD | Putative isovaleryl-CoA dehydrogenase protein | / | 0.453 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 5a3b | APR | SIR2 family protein | / | 0.453 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.452 | |
| 1c7o | PPG | Hemolysin | / | 0.452 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.452 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.452 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.452 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.452 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.452 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.452 | |
| 4iae | 1DX | Alr2278 protein | / | 0.452 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4v12 | POG | MaoC like domain protein | / | 0.451 | |
| 1gqt | ACP | Ribokinase | / | 0.450 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.450 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.450 | |
| 2i5b | ADP | Pyridoxine kinase | / | 0.450 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.450 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 4fi1 | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.450 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.448 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.448 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.447 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.447 | |
| 2xyu | Q9G | Ephrin type-A receptor 4 | 2.7.10.1 | 0.447 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.447 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.447 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 4yaw | 2AM | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.446 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.446 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.446 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.446 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.446 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.445 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.445 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.445 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.445 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.445 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.445 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.445 | |
| 3v2u | ATP | Protein GAL3 | / | 0.445 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 4iah | 1DX | Alr2278 protein | / | 0.445 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.445 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.444 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.444 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.444 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.444 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.444 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.444 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1kqn | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 2d1c | NAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.443 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.443 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.443 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.443 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4lfi | GNP | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 4rje | FNR | Lactate oxidase | / | 0.442 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.441 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.441 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.441 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.441 | |
| 3u9e | COA | Lmo1369 protein | / | 0.441 | |
| 4ijp | 1EH | Serine/threonine-protein kinase PRP4 homolog | 2.7.11.1 | 0.441 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.441 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.441 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.440 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.440 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.440 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.440 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.440 |