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 |
|---|---|---|---|
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 1.084 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 1.002 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 1.002 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.912 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.904 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.844 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.832 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.832 | |
| 5d2e | NAP | MlnE | / | 0.831 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.825 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.823 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.822 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.821 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.815 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.811 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.809 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.806 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.804 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.803 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.800 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.799 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.798 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.797 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.796 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.794 | |
| 3mje | NDP | AmphB | / | 0.791 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.789 | |
| 1sny | NAP | LD36273p | / | 0.788 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.787 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.786 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.784 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.782 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.775 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.773 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.770 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.769 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.769 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.769 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.767 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.767 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.766 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.766 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.765 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.764 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.764 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.762 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.760 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.760 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.759 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.759 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.758 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.758 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.757 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.756 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.756 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.756 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.755 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.755 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.753 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.753 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.753 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.752 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.752 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.747 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.744 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.744 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.744 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.742 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.742 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.742 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.742 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.741 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.741 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.740 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.739 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.739 | |
| 3uce | NDP | Dehydrogenase | / | 0.738 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.738 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.738 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.737 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.737 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.737 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.736 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.735 | |
| 4kwh | NAP | Reductase homolog | / | 0.735 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.734 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.733 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.733 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.733 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.732 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.732 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.731 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.731 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.730 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.727 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.727 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.727 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.725 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.724 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.723 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.722 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.722 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.722 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.721 | |
| 3sju | NDP | Keto reductase | / | 0.719 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.718 | |
| 4clo | NAP | Pteridine reductase | / | 0.718 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.718 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.717 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.716 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.715 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.715 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.714 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.714 | |
| 4qec | NAP | ElxO | / | 0.714 | |
| 4qed | NAP | ElxO | / | 0.714 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.713 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.713 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.712 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.711 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.711 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.710 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.710 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.709 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.709 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.709 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.708 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.707 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.705 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.705 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.703 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.703 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.703 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.703 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.702 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.702 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.701 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.701 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.701 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.701 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.700 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.700 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.700 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.699 | |
| 4hxy | NDP | Plm1 | / | 0.699 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.697 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.696 | |
| 1iy8 | NAD | Levodione reductase | / | 0.695 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.695 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.695 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.694 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.693 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.692 | |
| 4u7w | NDP | MxaA | / | 0.692 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.691 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.691 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.688 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.688 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.687 | |
| 3bmo | NAP | Pteridine reductase | / | 0.687 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.686 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.686 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.685 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.685 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.684 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.684 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.684 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.684 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.683 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.683 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.682 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.681 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.681 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.680 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.680 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.679 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.678 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.677 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.677 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.677 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.677 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.676 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.675 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.673 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.671 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.670 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.670 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.669 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.667 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.667 | |
| 2b36 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.665 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.665 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.665 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.664 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.663 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.663 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.662 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.661 | |
| 4qxm | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.661 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.660 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.660 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.660 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.658 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.657 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.657 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.655 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.655 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.654 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.654 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.653 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.653 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.653 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.650 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.650 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 |