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 |
|---|---|---|---|
| 3gx9 | TXD | Morphinone reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gx9 | TXD | Morphinone reductase | / | 1.000 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.487 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.485 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.477 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.476 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.476 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.474 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.471 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.471 | |
| 5a8e | XTK | Beta-1 adrenergic receptor | / | 0.470 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.468 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.468 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.468 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.467 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.466 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.465 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1ddt | APU | Diphtheria toxin | / | 0.464 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.462 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.461 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.460 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4n1f | CZH | Obelin | / | 0.460 | |
| 4tkg | 09L | Tankyrase-2 | 2.4.2.30 | 0.459 | |
| 3ny8 | JRZ | Beta-2 adrenergic receptor | / | 0.459 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.458 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.458 | |
| 1s36 | CEI | Obelin | / | 0.457 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.457 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.456 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.456 | |
| 4x3u | SVR | Chromobox protein homolog 7 | / | 0.456 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.455 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.454 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.454 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.454 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.453 | |
| 4l32 | 1VF | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.452 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.451 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.450 | |
| 1pj7 | FFO | Dimethylglycine oxidase | 1.5.3.10 | 0.450 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3f3y | 4OA | Bile salt sulfotransferase | 2.8.2.14 | 0.450 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.450 | |
| 3rga | ILD | Epoxide hydrolase LasB | 5.5.1 | 0.449 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.448 | |
| 2de4 | BPS | 2'-hydroxybiphenyl-2-sulfinate desulfinase | 3.13.1.3 | 0.448 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.448 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3nya | JTZ | Beta-2 adrenergic receptor | / | 0.448 | |
| 4fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 4fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.447 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 3qen | 5BT | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1vfs | DCS | Alanine racemase | / | 0.445 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.445 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 1jf0 | CZH | Obelin | / | 0.444 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.444 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.444 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 4hlm | 16S | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1qv0 | CZH | Obelin | / | 0.443 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.443 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.443 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.443 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.443 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2aov | C2M | Histamine N-methyltransferase | 2.1.1.8 | 0.442 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.442 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.442 | |
| 2wea | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.441 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.440 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.440 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.440 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4mrx | CZH | Obelin | / | 0.440 | |
| 4nqg | CZH | Mitrocomin | / | 0.440 |