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 |
|---|---|---|---|
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 1.476 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 1.088 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 1.009 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.988 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.957 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.950 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.929 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.901 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.899 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.894 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.889 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.885 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.880 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.877 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.856 | |
| 1iy8 | NAD | Levodione reductase | / | 0.855 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.854 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.848 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.845 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.844 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.843 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.843 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.843 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.842 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.836 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.834 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.834 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.832 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.827 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.825 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.823 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.822 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.822 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.817 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.815 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.815 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.813 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.812 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.810 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.809 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.808 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.806 | |
| 1sny | NAP | LD36273p | / | 0.806 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.805 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.805 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.805 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.802 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.798 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.798 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.797 | |
| 4kwh | NAP | Reductase homolog | / | 0.795 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.794 | |
| 3sju | NDP | Keto reductase | / | 0.794 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.789 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.788 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.788 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.785 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.783 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.781 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.781 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.780 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.779 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.778 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.778 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.776 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.775 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.775 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.775 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.773 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.773 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.773 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.772 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.769 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.768 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.765 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.764 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.764 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.763 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.760 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.760 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.758 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.757 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.757 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.753 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.751 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.749 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.749 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.748 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.746 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.746 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.746 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.745 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.745 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.743 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.740 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.740 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.740 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.740 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.739 | |
| 4qed | NAP | ElxO | / | 0.739 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.737 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.737 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.736 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.736 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.735 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.732 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.732 | |
| 5d2e | NAP | MlnE | / | 0.730 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.729 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.728 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.728 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.727 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.727 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.725 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.722 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.720 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.719 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.719 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.715 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.714 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.713 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.711 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.710 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.708 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.706 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.705 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.704 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.703 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.703 | |
| 3mje | NDP | AmphB | / | 0.702 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.697 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.697 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.697 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.697 | |
| 4hxy | NDP | Plm1 | / | 0.695 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.695 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.692 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.692 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.692 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.691 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.690 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.690 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.689 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.689 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.687 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.687 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.687 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.686 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.686 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.686 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.685 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.685 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.685 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.684 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.684 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.683 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.682 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.682 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.681 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.681 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.680 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.679 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.679 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.677 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.677 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.676 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.676 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.673 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.673 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.672 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.672 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.670 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.669 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.669 | |
| 3ec7 | NAD | Inositol 2-dehydrogenase | / | 0.668 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.668 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.668 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.666 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.665 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.663 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.662 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.662 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.660 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.658 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.657 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.657 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.654 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.654 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.653 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.652 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.652 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.651 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.651 |