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 |
|---|---|---|---|
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 1.122 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.954 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.932 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.930 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.914 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.892 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.886 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.883 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.879 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.875 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.867 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.864 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.860 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.858 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.857 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.856 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.840 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.831 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.830 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.826 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.823 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.818 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.817 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.817 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.816 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.816 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.815 | |
| 4kwh | NAP | Reductase homolog | / | 0.814 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.809 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.807 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.807 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.805 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.805 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.804 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.804 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.801 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.801 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.798 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.796 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.796 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.795 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.792 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.791 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.790 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.789 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.789 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.784 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.784 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.783 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.782 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.782 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.780 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.780 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.780 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.779 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.773 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.772 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.772 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.769 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.766 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.762 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.760 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.760 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.760 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.758 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.757 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.753 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.752 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.752 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.751 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.751 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.750 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.749 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.748 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.748 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.747 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.747 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.747 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.745 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.745 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.745 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.744 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.742 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.738 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.737 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.733 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.732 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.732 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.731 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.730 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.730 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.729 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.728 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.728 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.727 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.726 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.725 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.725 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.725 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.725 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.723 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.722 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.722 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.721 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.720 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.720 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.720 | |
| 4qec | NAP | ElxO | / | 0.720 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.719 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.717 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.717 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.717 | |
| 3sju | NDP | Keto reductase | / | 0.715 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.714 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.712 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.711 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.710 | |
| 4hxy | NDP | Plm1 | / | 0.710 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.710 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.708 | |
| 3mje | NDP | AmphB | / | 0.707 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.707 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.703 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.702 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.702 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.702 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.699 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.698 | |
| 4clo | NAP | Pteridine reductase | / | 0.698 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.697 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.697 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.696 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.695 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.695 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.695 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.695 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.694 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.694 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.693 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.693 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.693 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.692 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.692 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.691 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.691 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.691 | |
| 1iy8 | NAD | Levodione reductase | / | 0.690 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.689 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.688 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.686 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.686 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.685 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.684 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.683 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.683 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.683 | |
| 1sny | NAP | LD36273p | / | 0.679 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.676 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.676 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.676 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.676 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.675 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.675 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.674 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.674 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.673 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.672 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.672 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.672 | |
| 5d2e | NAP | MlnE | / | 0.672 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.671 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.671 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.671 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.671 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.670 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.670 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.669 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.669 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.669 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.668 | |
| 3bmo | NAP | Pteridine reductase | / | 0.668 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.668 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.667 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.667 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.667 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.667 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.667 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.667 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.667 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.666 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.665 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.665 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.665 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.664 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.664 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.663 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.662 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.662 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.661 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.661 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.659 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.658 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.658 | |
| 4u7w | NDP | MxaA | / | 0.658 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.657 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.657 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.657 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.657 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.656 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 4qed | NAP | ElxO | / | 0.655 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.653 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.653 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.652 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.652 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.651 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.651 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 |