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 |
|---|---|---|---|
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 1.141 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.940 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.940 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.912 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.862 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.836 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.819 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.818 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.812 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.807 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.801 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.801 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.800 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.799 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.795 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.795 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.794 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.791 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.788 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.787 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.785 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.782 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.780 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.779 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.775 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.775 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.774 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.773 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.772 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.772 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.772 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.768 | |
| 1sny | NAP | LD36273p | / | 0.768 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.768 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.767 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.766 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.764 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.763 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.763 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.760 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.760 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.757 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.753 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.753 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.752 | |
| 4hxy | NDP | Plm1 | / | 0.752 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.751 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.751 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.749 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.747 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.745 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.745 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.744 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.744 | |
| 5d2e | NAP | MlnE | / | 0.743 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.743 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.741 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.741 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.738 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.737 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.737 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.737 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.735 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.734 | |
| 3mje | NDP | AmphB | / | 0.732 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.731 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.731 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.730 | |
| 4kwh | NAP | Reductase homolog | / | 0.729 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.728 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.727 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.726 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.724 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.724 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.724 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.723 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.723 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.722 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.722 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.722 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.721 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.721 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.721 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.721 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.720 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.720 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.720 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.717 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.717 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.715 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.715 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.714 | |
| 3sju | NDP | Keto reductase | / | 0.714 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.713 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.712 | |
| 3uce | NDP | Dehydrogenase | / | 0.712 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.711 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.710 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.710 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.710 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.707 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.707 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.706 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.705 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.705 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.705 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.704 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.704 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.703 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.703 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.699 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.699 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.698 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.698 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.696 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.696 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.695 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.695 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.695 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.693 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.693 | |
| 1qyx | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.691 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.691 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.691 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.690 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.690 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.690 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.689 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.689 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.689 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.689 | |
| 4qxm | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.689 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.688 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.688 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.688 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.687 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.686 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.686 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.685 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.685 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.685 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.684 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.681 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.680 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.680 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.679 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.679 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.678 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.678 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.677 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.677 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.675 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.674 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.673 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.672 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.672 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.672 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.671 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.671 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.671 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.670 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.670 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.670 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.669 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.669 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.669 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.668 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.668 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.667 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.667 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.667 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.667 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.667 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.666 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.665 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.663 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.663 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.661 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.661 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.661 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.660 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.660 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.660 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.659 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.659 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.659 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.659 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.658 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.656 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.655 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.655 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.654 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.653 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.653 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.652 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.651 |