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 |
|---|---|---|---|
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.171 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.147 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.094 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.082 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.078 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.038 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.037 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.034 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.033 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.027 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.012 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.007 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.002 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.990 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.986 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.963 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.958 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.957 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.951 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.947 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.927 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.926 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.921 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.900 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.898 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.885 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.868 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.864 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.861 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.859 | |
| 2b36 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.854 | |
| 4qxm | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.851 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.843 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.799 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.792 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.791 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.788 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.783 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.783 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.781 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.778 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.777 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.773 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.771 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.768 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.762 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.762 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.761 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.760 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.755 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.754 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.749 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.745 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.744 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.743 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.743 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.742 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.740 | |
| 1enp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.740 | |
| 1sny | NAP | LD36273p | / | 0.739 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.738 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.737 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.737 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.736 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.736 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.731 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.731 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.731 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.730 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.729 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.729 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.728 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.727 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.725 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.725 | |
| 4hxy | NDP | Plm1 | / | 0.724 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.723 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.720 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.720 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.719 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.719 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.718 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.717 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.715 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.715 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.715 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.715 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.715 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.712 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.712 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.712 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.711 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.711 | |
| 3mje | NDP | AmphB | / | 0.711 | |
| 4kwh | NAP | Reductase homolog | / | 0.711 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.710 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.710 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.708 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.707 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.706 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.705 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.704 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.704 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.703 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.702 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.702 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.701 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.700 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.700 | |
| 4u7w | NDP | MxaA | / | 0.700 | |
| 4qec | NAP | ElxO | / | 0.699 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.698 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.698 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.698 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.697 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.697 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.697 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.695 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.695 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.694 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.694 | |
| 4clo | NAP | Pteridine reductase | / | 0.693 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.691 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.691 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.690 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.690 | |
| 4qed | NAP | ElxO | / | 0.690 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.689 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.688 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.688 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.688 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.688 | |
| 1iy8 | NAD | Levodione reductase | / | 0.687 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.687 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.687 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.687 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.686 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.686 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.685 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.685 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.684 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.684 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.684 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.683 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.683 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.682 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.682 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.681 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.681 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.681 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.679 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.678 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.677 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.677 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.676 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.676 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.674 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.673 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.673 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.673 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.672 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.672 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.672 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.671 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.670 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.670 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.670 | |
| 5d2e | NAP | MlnE | / | 0.670 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.669 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.669 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.669 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.669 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.668 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.667 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.667 | |
| 3sju | NDP | Keto reductase | / | 0.666 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.665 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.665 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.663 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.662 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.662 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.661 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.661 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.659 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.659 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.659 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.659 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.659 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.658 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.657 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.656 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.655 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.655 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.655 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.654 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.654 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.654 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.654 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.653 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.653 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.653 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.653 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.653 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.652 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.652 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.652 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.652 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.652 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.651 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.651 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.650 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.650 |