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 |
|---|---|---|---|
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 1.375 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.926 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.906 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.841 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.837 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.833 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.817 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.814 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.812 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.805 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.803 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.796 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.796 | |
| 3sju | NDP | Keto reductase | / | 0.785 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.785 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.784 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.784 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.775 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.775 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.774 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.771 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.770 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.768 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.766 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.766 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.766 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.765 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.760 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.755 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.754 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.753 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.752 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.752 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.752 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.749 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.749 | |
| 3mje | NDP | AmphB | / | 0.749 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.749 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.744 | |
| 1sny | NAP | LD36273p | / | 0.740 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.738 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.737 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.736 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.735 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.733 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.732 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.731 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.730 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.729 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.728 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.728 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.726 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.726 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.725 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.725 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.724 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.722 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.721 | |
| 3baz | NAP | Hydroxyphenylpyruvate reductase | 1.1.1.237 | 0.720 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.720 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.720 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.719 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.716 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.716 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.715 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.714 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.713 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.712 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.710 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.709 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.708 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.707 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.706 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.706 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.706 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.706 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.706 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.705 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.705 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.705 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.705 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.704 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.703 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.703 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.702 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.702 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.701 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.701 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.701 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.700 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.700 | |
| 5d2e | NAP | MlnE | / | 0.700 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.698 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.698 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.695 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.695 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.695 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.693 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.692 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.692 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.691 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.691 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.690 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.690 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.687 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.687 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.686 | |
| 3uce | NDP | Dehydrogenase | / | 0.686 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.685 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.685 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.683 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.683 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.683 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.683 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.682 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.681 | |
| 1ptj | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.681 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.681 | |
| 4hxy | NDP | Plm1 | / | 0.681 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.680 | |
| 4kwh | NAP | Reductase homolog | / | 0.680 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.679 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.678 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.678 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.678 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.676 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.676 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.676 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.675 | |
| 1d4o | NAP | NAD(P) transhydrogenase, mitochondrial | / | 0.674 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.674 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.673 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.671 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.671 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.670 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.670 | |
| 4l4x | NDP | AmphI | / | 0.669 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.668 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.668 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.668 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.667 | |
| 1f28 | UMP | Thymidylate synthase | 2.1.1.45 | 0.667 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.667 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.667 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.665 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.665 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.665 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.665 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.664 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.663 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.663 | |
| 1hy3 | PPS | Estrogen sulfotransferase | 2.8.2.4 | 0.662 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.662 | |
| 4fox | UMP | Thymidylate synthase ThyA | / | 0.662 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.661 | |
| 4dq1 | UMP | Thymidylate synthase | / | 0.661 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.658 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.658 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.657 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.657 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.657 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.657 | |
| 4qed | NAP | ElxO | / | 0.657 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.657 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.655 | |
| 1b5d | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.654 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.654 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.654 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.654 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.654 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.653 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.653 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.653 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.651 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.651 |