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 |
|---|---|---|---|
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 1.000 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.629 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.597 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.594 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.581 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.580 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.573 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.564 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.552 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.549 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.544 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.543 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.542 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.538 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.537 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.531 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.525 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.524 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.518 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.511 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.511 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.510 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.507 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.506 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.502 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.499 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.499 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.495 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.488 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 8dfr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.483 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.481 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.481 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.477 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.476 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.476 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.474 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.474 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.473 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.473 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.471 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.467 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.466 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.465 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.464 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.464 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.464 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.464 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.464 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.463 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.463 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.463 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.462 | |
| 5dp2 | NAP | CurF | / | 0.462 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.460 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.459 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.459 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.458 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.458 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.457 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.457 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.457 | |
| 4lnb | ED5 | CaaX farnesyltransferase beta subunit Ram1 | / | 0.457 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.456 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.455 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.455 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.454 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.453 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.453 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.452 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.452 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.452 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.452 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.451 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.450 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.450 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.450 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.450 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.449 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.449 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.449 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.449 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.448 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.448 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.447 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.447 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.447 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.447 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.447 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.446 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.446 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.445 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.445 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.445 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.445 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.445 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.445 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.445 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.444 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.444 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.444 | |
| 3nbv | ANP | Ketohexokinase | / | 0.444 | |
| 3r95 | ACO | MccE protein | / | 0.444 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.444 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.443 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.443 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.443 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.442 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.442 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.441 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.441 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.441 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.441 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.441 | |
| 4dja | FAD | (6-4) photolyase | / | 0.441 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.441 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.440 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.440 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.440 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 |