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 |
|---|---|---|---|
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 1.000 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.596 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.589 | |
| 1tyt | FAD | Trypanothione reductase | 1.8.1.12 | 0.575 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.575 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.573 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.570 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.556 | |
| 4kpr | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.545 | |
| 1dnc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.530 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.516 | |
| 1gxf | FAD | Trypanothione reductase | 1.8.1.12 | 0.484 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.482 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.470 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.467 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.467 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.466 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.464 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.463 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.463 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.463 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.462 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.462 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.462 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.461 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.460 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.459 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.458 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.458 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.458 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.458 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.458 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.457 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.457 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.456 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.455 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.455 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.455 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.455 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.455 | |
| 5dp2 | NAP | CurF | / | 0.455 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.455 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.454 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.454 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.454 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.454 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.454 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.453 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3iaa | TYD | CalG2 | / | 0.453 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.453 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.453 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4l4x | NDP | AmphI | / | 0.453 | |
| 5doz | NDP | JamJ | / | 0.453 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.452 | |
| 1gqt | ACP | Ribokinase | / | 0.452 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.452 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.451 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.451 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.451 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.451 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.449 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.449 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.448 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.448 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.448 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.448 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.448 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.448 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.448 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.447 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.447 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.447 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.447 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.447 | |
| 1iy8 | NAD | Levodione reductase | / | 0.446 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.446 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.446 | |
| 3eks | CY9 | Actin-5C | / | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.445 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.445 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.445 | |
| 2emr | SAH | Diphthine synthase | / | 0.445 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.445 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.444 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.444 | |
| 2dsg | SAH | Diphthine synthase | / | 0.444 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.444 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.444 | |
| 3ieu | GDP | GTPase Era | / | 0.444 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.444 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.444 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.443 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.443 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.443 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.443 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.443 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.443 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.442 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.442 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.442 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.442 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.442 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.441 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.441 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.441 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.440 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.440 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 2e07 | SAH | Diphthine synthase | / | 0.440 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.440 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.440 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.440 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.440 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.440 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.440 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.440 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.440 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 |