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 |
|---|---|---|---|
| 4f6r | GDP | Tubulin beta chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4f6r | GDP | Tubulin beta chain | / | 1.000 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.585 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.506 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.505 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.500 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.484 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.475 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.475 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.474 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 0.474 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.472 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.471 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.470 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.469 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.467 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.466 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.466 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.464 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.464 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.462 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.461 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.461 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.461 | |
| 5a3b | APR | SIR2 family protein | / | 0.461 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.460 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.460 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.460 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.459 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.458 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.458 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.456 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.456 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.455 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.455 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.455 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.455 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.455 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.455 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 0.455 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.454 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.454 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.453 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.453 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.453 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.453 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.452 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.451 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.451 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.451 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.451 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.450 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.450 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.450 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.450 | |
| 1feb | FAD | Trypanothione reductase | 1.8.1.12 | 0.449 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.449 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.449 | |
| 2bto | GTP | Tubulin | / | 0.449 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.449 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.449 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.449 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.449 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.449 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.448 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.448 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.447 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.447 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.447 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.447 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.447 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.447 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.447 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.447 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.447 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.446 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.446 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.446 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.446 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.446 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.445 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.445 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.445 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.445 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.445 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.445 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.445 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.444 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.444 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.444 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.444 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 1aa6 | MGD | Formate dehydrogenase H | 1.1.99.33 | 0.443 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.443 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.443 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.443 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.443 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.443 | |
| 4o4l | GTP | Tubulin alpha-1B chain | / | 0.443 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.442 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.442 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.442 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.442 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.442 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4blr | UTP | NTPase P4 | / | 0.442 | |
| 4ei7 | GDP | Plasmid replication protein RepX | / | 0.442 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.442 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.441 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.441 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.441 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.441 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 3ryh | GTP | Tubulin alpha chain | / | 0.441 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.441 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.441 | |
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 0.441 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.440 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.440 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.440 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3coz | 54H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.440 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.440 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 |