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 |
|---|---|---|---|
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 1.000 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.508 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.505 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.504 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.490 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.489 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.488 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.486 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.485 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.483 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.482 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.481 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.481 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.479 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.476 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.475 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.475 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.475 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.474 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.474 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.473 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.472 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.471 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.470 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.469 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.468 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.467 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.466 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.466 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.465 | |
| 4lez | 1SY | Cyclic GMP-AMP synthase | / | 0.464 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.463 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.463 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.463 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.463 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.462 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.462 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.462 | |
| 2ejz | SAH | Diphthine synthase | / | 0.461 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.461 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.461 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.461 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.461 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.460 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.459 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.458 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.458 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.457 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.457 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.456 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.455 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.455 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.454 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.454 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.454 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4tm4 | FDA | KtzI | / | 0.454 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.453 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.453 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3ieu | GDP | GTPase Era | / | 0.453 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.453 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.451 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.451 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.450 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.450 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.450 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.450 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.449 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.449 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.449 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.449 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.449 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.449 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.448 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.448 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.448 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.448 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.448 | |
| 3eku | CY9 | Actin-5C | / | 0.448 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.448 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.448 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.448 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.448 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.447 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.447 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.447 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.447 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.447 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.447 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.447 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.447 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.447 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.446 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.446 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.446 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.445 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.445 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.445 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.445 | |
| 4qak | 2AM | RNA 2',3'-cyclic phosphodiesterase | / | 0.445 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.445 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.445 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.444 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.444 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.444 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.444 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.443 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.443 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.443 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4hcy | 0YN | Transketolase | / | 0.443 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.443 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.443 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.442 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.442 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.442 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.442 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.441 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.441 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.441 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.440 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.440 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.440 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.440 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.440 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.440 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.440 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.440 | |
| 2y4g | TIR | TamL | / | 0.440 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 |