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 |
|---|---|---|---|
| 5bu2 | ADP | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5bu2 | ADP | Uncharacterized protein | / | 1.000 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.500 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.484 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.484 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.484 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.480 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.474 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.474 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.471 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.470 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.469 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.469 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.468 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.468 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.467 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.467 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.466 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.466 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.464 | |
| 4z87 | GDP | Inosine-5'-monophosphate dehydrogenase | / | 0.464 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.463 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.460 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.460 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.460 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.460 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.459 | |
| 4h6p | FMN | Chromate reductase | / | 0.459 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.459 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.458 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.458 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.457 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.456 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 4j7g | TRH | PCZA361.3 | / | 0.456 | |
| 4xo7 | ASD | Aldo-keto reductase family 1 member C2 | / | 0.456 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.455 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.455 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.455 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.455 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.455 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.454 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.453 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.452 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 1dia | L24 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.451 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.451 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.450 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.450 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.449 | |
| 2pcm | SAH | Diphthine synthase | / | 0.449 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.448 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.448 | |
| 3abx | RCB | Glucanase | / | 0.448 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.448 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.448 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2e8s | SAH | Diphthine synthase | / | 0.447 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.447 | |
| 4j7h | TRH | PCZA361.3 | / | 0.447 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.446 | |
| 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 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.446 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4phl | PIL | Phosphodiesterase | / | 0.446 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.446 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.446 | |
| 1gaq | FAD | Ferredoxin | / | 0.445 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.445 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.445 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.445 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.445 | |
| 4eqs | COA | Coenzyme A disulfide reductase | / | 0.445 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.444 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.444 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.444 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.444 | |
| 4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2emr | SAH | Diphthine synthase | / | 0.443 | |
| 1o1t | 2NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1qrt | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.442 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.442 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.442 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 4fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 4fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.441 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.441 | |
| 3tfy | MET_LEU_GLY_PRO | N-alpha-acetyltransferase 50 | 2.3.1 | 0.441 | |
| 3ts1 | TYA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.441 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 1kfc | IPL | Tryptophan synthase alpha chain | / | 0.440 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.440 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 3w5u | FAD | Ferredoxin | / | 0.440 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.440 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 |