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 |
|---|---|---|---|
| 1yy5 | FAD | Polyamine oxidase FMS1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1yy5 | FAD | Polyamine oxidase FMS1 | / | 1.000 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.592 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.580 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.563 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.552 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.550 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.548 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.547 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.542 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.537 | |
| 1tdn | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.528 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.528 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.527 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.526 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.526 | |
| 3rha | FDA | Putrescine oxidase | / | 0.516 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.514 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.513 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.512 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.510 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.507 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.506 | |
| 3ka7 | FAD | Putative oxidoreductase | / | 0.504 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.492 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.492 | |
| 4i9u | 1E7 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.492 | |
| 3kve | FAD | L-amino-acid oxidase | / | 0.491 | |
| 2ba9 | FAD | Putative aminooxidase | / | 0.487 | |
| 1l7e | NAI | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.486 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.483 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.480 | |
| 3hdy | FAD | UDP-galactopyranose mutase | / | 0.480 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.478 | |
| 3t7o | UPG | Glycogenin-1 | 2.4.1.186 | 0.478 | |
| 3q2k | NAI | Probable oxidoreductase | / | 0.473 | |
| 3u2x | ASO | Glycogenin-1 | 2.4.1.186 | 0.473 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.469 | |
| 4wq5 | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.468 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.467 | |
| 5j3w | FMN | Sensory box protein | / | 0.466 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.464 | |
| 2gs7 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.463 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.462 | |
| 3tdk | NAD | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.462 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.461 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.460 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.460 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.459 | |
| 2yis | YIS | Mitogen-activated protein kinase 14 | / | 0.458 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.458 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.458 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.457 | |
| 3hdy | FDA | UDP-galactopyranose mutase | / | 0.457 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.457 | |
| 4gap | NAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.457 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.456 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.455 | |
| 2zmd | 537 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.455 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.455 | |
| 3p23 | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.455 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.455 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.453 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.453 | |
| 1ofg | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.452 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.452 | |
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.452 | |
| 3qj4 | FAD | Renalase | / | 0.452 | |
| 3vry | B43 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.452 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.451 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.451 | |
| 4iac | ACP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.451 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.450 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.450 | |
| 2dji | FAD | Pyruvate oxidase | / | 0.450 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 4h4y | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.450 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 4s26 | SAH | Phosphomethylpyrimidine synthase, chloroplastic | 4.1.99.17 | 0.449 | |
| 4xw4 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.449 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.448 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 5j4e | FMN | Sensory box protein | / | 0.448 | |
| 1pno | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.447 | |
| 1znq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.447 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.447 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.447 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.447 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.447 | |
| 2bab | FAD | Putative aminooxidase | / | 0.446 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.446 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.446 | |
| 4c2u | ANP | DNA helicase | / | 0.446 | |
| 4ju1 | 1NZ | Genome polyprotein | 2.7.7.48 | 0.446 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.445 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.445 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.445 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.444 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.444 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.443 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.443 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.442 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.442 | |
| 3a5m | ATP | Major actin | / | 0.442 | |
| 4bi0 | Z0W | Dual specificity protein kinase TTK | 2.7.12.1 | 0.442 | |
| 4hse | ADP | Chaperone protein ClpB | / | 0.442 | |
| 4k2r | ANP | Tyrosine-protein kinase ZAP-70 | 2.7.10.2 | 0.442 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.441 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.441 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.441 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 4rrw | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 4rrz | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.441 | |
| 1f3p | FAD | Ferredoxin reductase | / | 0.440 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.440 | |
| 3mhy | ATP | Nitrogen regulatory protein P-II 1 | / | 0.440 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.440 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.440 | |
| 4dg3 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |