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 |
|---|---|---|---|
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.603 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.582 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.567 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.566 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.546 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.526 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.515 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.501 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.497 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.497 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.494 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.487 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.475 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 4j7g | TRH | PCZA361.3 | / | 0.474 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.471 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.471 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.464 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.463 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3hxf | BD9 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.462 | |
| 4lut | DCS | Alanine racemase | / | 0.462 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.459 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.459 | |
| 4j7h | TRH | PCZA361.3 | / | 0.458 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.458 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.455 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.455 | |
| 2ejz | SAH | Diphthine synthase | / | 0.455 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 4e2y | JHZ | Methyltransferase | / | 0.454 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.452 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.451 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2xnv | VU3 | Soluble acetylcholine receptor | / | 0.449 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.448 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.448 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.447 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.447 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.447 | |
| 5d4v | YGP | Uncharacterized protein MJ0489 | / | 0.447 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.446 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.445 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.444 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.443 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 2wea | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.443 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.443 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.443 | |
| 1ld8 | U49 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.442 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3nlj | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.442 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.441 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 5ds3 | 09L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.440 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.440 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.440 |