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 |
|---|---|---|---|
| 3ilt | TRU | Glutamate receptor 2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ilt | TRU | Glutamate receptor 2 | / | 1.000 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.620 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.612 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.519 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.494 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.494 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.488 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.485 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.481 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.481 | |
| 3ieu | GDP | GTPase Era | / | 0.480 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.477 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.477 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.475 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.475 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.474 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.473 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 3rn8 | RN8 | Glutamate receptor 2 | / | 0.471 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.470 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.470 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.470 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.469 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.469 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.469 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 2ejz | SAH | Diphthine synthase | / | 0.466 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.465 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.464 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.464 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.464 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.464 | |
| 3uce | NDP | Dehydrogenase | / | 0.464 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.464 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.463 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.463 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.463 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2p6k | SAH | Diphthine synthase | / | 0.462 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.462 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.462 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.462 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.461 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.461 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.461 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.461 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.461 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.460 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.460 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.460 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.459 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.459 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.459 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.459 | |
| 5ifi | PRX | Acetyl-coenzyme A synthetase | / | 0.459 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.458 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3a3g | DLZ | Lumazine protein | / | 0.458 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.458 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.458 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.458 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.457 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.457 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.457 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.456 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.456 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.456 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.456 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.455 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.455 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.455 | |
| 4h1v | GNP | Dynamin-1-like protein | 3.6.5.5 | 0.455 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.455 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.455 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.454 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.454 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 3mje | NDP | AmphB | / | 0.454 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.454 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.453 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.453 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.453 | |
| 2o12 | FMN | Chorismate synthase | / | 0.453 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 3ge6 | FMN | Nitroreductase | / | 0.453 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.453 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.452 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.452 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.452 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.452 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.452 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.451 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.451 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.451 | |
| 2ejj | SAH | Diphthine synthase | / | 0.451 | |
| 2owk | SAH | Diphthine synthase | / | 0.451 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.451 | |
| 4ynt | FDA | Glucose oxidase, putative | / | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.450 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.450 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.450 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.450 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.450 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.450 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.449 | |
| 2e07 | SAH | Diphthine synthase | / | 0.449 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.449 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.449 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.449 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.448 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.448 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.448 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.448 | |
| 4rpj | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.448 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1iy8 | NAD | Levodione reductase | / | 0.447 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.447 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.447 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.447 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.447 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.447 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.447 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.447 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.446 | |
| 2hut | SAH | Diphthine synthase | / | 0.446 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.446 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.446 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 4u0m | ATP | Cyclic GMP-AMP synthase | / | 0.446 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.445 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 2dxw | SAH | Diphthine synthase | / | 0.445 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.445 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.445 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.445 | |
| 3iaa | TYD | CalG2 | / | 0.445 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.445 | |
| 1t4c | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.444 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.444 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.444 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.444 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.444 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.444 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.443 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.443 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.443 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.443 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.443 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.443 | |
| 2owf | SAH | Diphthine synthase | / | 0.443 | |
| 2p6d | SAH | Diphthine synthase | / | 0.443 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.443 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.443 | |
| 3wag | TYD | Glycosyltransferase | / | 0.443 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.442 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.442 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.442 | |
| 2ehl | SAH | Diphthine synthase | / | 0.442 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.442 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 3u9e | COA | Lmo1369 protein | / | 0.442 | |
| 4aqc | 88A | Tyrosine-protein kinase JAK2 | / | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.442 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.441 | |
| 2emu | SAH | Diphthine synthase | / | 0.441 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.441 | |
| 2rc4 | ACO | Histone acetyltransferase KAT6A | / | 0.441 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.441 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.441 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.441 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.441 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.440 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.440 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.440 | |
| 2p5f | SAH | Diphthine synthase | / | 0.440 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.440 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.440 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.440 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.440 |