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 Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 1.259 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.873 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.862 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.841 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.830 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.817 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.811 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.806 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.805 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.804 | |
| 4u7w | NDP | MxaA | / | 0.800 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.798 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.796 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.794 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.792 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.791 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.788 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.780 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.778 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.778 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.775 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.774 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.774 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.774 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.771 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.770 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.769 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.768 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.767 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.766 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.764 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.762 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.759 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.755 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.754 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.754 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.754 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.753 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.752 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.751 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.751 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.750 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.749 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.749 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.749 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.747 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.747 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.746 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.746 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.745 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.745 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.745 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.743 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.742 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.741 | |
| 4kwh | NAP | Reductase homolog | / | 0.741 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.741 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.741 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.739 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.739 | |
| 1iy8 | NAD | Levodione reductase | / | 0.738 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.738 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.737 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.737 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.735 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.735 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.734 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.734 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.734 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.731 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.730 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.730 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.728 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.727 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.727 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.726 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.726 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.723 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.722 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.721 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.721 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.720 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.720 | |
| 4hxy | NDP | Plm1 | / | 0.719 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.718 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.714 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.713 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.712 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.712 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.712 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.711 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.710 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.710 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.710 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.709 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.709 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.708 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.708 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.708 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.708 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.708 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.707 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.705 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.705 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.702 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.701 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.699 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.698 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.698 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.698 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.697 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.696 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.696 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.695 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.695 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.694 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.694 | |
| 3sju | NDP | Keto reductase | / | 0.693 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.693 | |
| 1sny | NAP | LD36273p | / | 0.692 | |
| 5d2e | NAP | MlnE | / | 0.692 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.691 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.691 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.691 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.690 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.689 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.688 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.686 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.685 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.685 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.685 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.685 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.685 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.684 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.683 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.682 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.682 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.681 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.681 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.681 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.681 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.681 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.680 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.680 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.679 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.678 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.678 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.678 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.678 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.675 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.675 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.675 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.673 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.673 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.673 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.672 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.670 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.670 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.669 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.669 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.669 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.668 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.668 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.668 | |
| 2bry | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.667 | |
| 2pa3 | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.667 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.667 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.666 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.665 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.665 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.665 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.665 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.665 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.664 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.664 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.663 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.663 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.663 | |
| 5je4 | SAH | Methyl transferase | / | 0.663 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.662 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.661 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.661 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.661 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.660 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.660 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.660 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.659 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.659 | |
| 2jg7 | NAD | Antiquitin | / | 0.658 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.658 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.658 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.657 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.657 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.657 | |
| 4gf5 | SAH | CalS11 | / | 0.656 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.655 | |
| 3mje | NDP | AmphB | / | 0.655 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.655 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.654 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.654 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.654 | |
| 4rdi | ATP | tRNA threonylcarbamoyladenosine dehydratase | 6.1 | 0.654 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.653 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.652 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.652 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.652 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.651 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.651 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.651 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 |