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 |
|---|---|---|---|
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 1.223 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.880 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.873 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.868 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.865 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.856 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.849 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.843 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.843 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.837 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.837 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.834 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.830 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.825 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.821 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.820 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.815 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.814 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.813 | |
| 4kwh | NAP | Reductase homolog | / | 0.811 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.806 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.805 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.804 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.802 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.799 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.798 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.797 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.793 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.788 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.788 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.788 | |
| 3uce | NDP | Dehydrogenase | / | 0.788 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.786 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.783 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.782 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.782 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.781 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.781 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.781 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.780 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.778 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.772 | |
| 4u7w | NDP | MxaA | / | 0.771 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.769 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.769 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.769 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.766 | |
| 3sju | NDP | Keto reductase | / | 0.765 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.764 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.764 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.763 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.763 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.761 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.760 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.760 | |
| 4hxy | NDP | Plm1 | / | 0.760 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.759 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.758 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.758 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.758 | |
| 5d2e | NAP | MlnE | / | 0.758 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.757 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.757 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.755 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.754 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.752 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.751 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.750 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.750 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.750 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.749 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.749 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.747 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.746 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.746 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.746 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.745 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.745 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.744 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.744 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.743 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.741 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.740 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.739 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.739 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.739 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.739 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.739 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.738 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.737 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.737 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.736 | |
| 1sny | NAP | LD36273p | / | 0.733 | |
| 3mje | NDP | AmphB | / | 0.733 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.732 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.730 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.730 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.728 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.728 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.727 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.727 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.726 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.725 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.725 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.723 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.723 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.723 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.721 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.720 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.720 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.720 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.719 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.718 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.718 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.717 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.717 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.717 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.714 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.713 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.713 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.712 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.710 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.710 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.709 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.709 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.708 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.708 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.707 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.707 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.706 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.706 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.705 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.705 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.704 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.704 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.703 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.701 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.700 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.696 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.696 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.696 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.695 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.693 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.693 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.692 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.691 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.691 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.690 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.688 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.688 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.688 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.687 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.687 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.687 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.687 | |
| 3au8 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.686 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.686 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.686 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.684 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.684 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.684 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.684 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.684 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.683 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.683 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.683 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.682 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.682 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.681 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.680 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.680 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.680 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.680 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.680 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.679 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.676 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.676 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.676 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.675 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.674 | |
| 4qed | NAP | ElxO | / | 0.674 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.673 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.672 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.672 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.672 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.671 | |
| 3ras | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.670 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.670 | |
| 4qec | NAP | ElxO | / | 0.670 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.669 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.668 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.668 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.667 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.666 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.666 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.666 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.666 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.665 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.664 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.664 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.662 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.662 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.662 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.661 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.660 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.660 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.659 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.658 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.658 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.658 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.658 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.658 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.656 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.654 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.653 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.653 | |
| 4dqu | NAI | 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 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.650 |