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 |
|---|---|---|---|
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 1.486 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 1.286 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 1.245 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.996 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.933 | |
| 4u7w | NDP | MxaA | / | 0.873 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.853 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.824 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.824 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.817 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.801 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.799 | |
| 3pdu | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.795 | |
| 4hxy | NDP | Plm1 | / | 0.794 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.792 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.788 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.787 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.782 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.781 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.777 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.777 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.772 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.772 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.766 | |
| 3uce | NDP | Dehydrogenase | / | 0.766 | |
| 5d2e | NAP | MlnE | / | 0.766 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.763 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.761 | |
| 3mje | NDP | AmphB | / | 0.759 | |
| 1sny | NAP | LD36273p | / | 0.755 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.755 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.753 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.752 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.750 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.750 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.749 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.747 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.746 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.746 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.740 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.739 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.731 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.730 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.726 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.726 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.725 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.725 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.724 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.724 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.722 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.721 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.720 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.719 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.719 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.718 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.717 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.716 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.715 | |
| 1wp4 | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.713 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.713 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.710 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.709 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.708 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.708 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.706 | |
| 4qec | NAP | ElxO | / | 0.706 | |
| 3sju | NDP | Keto reductase | / | 0.705 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.703 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.703 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.703 | |
| 4aic | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.702 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.702 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.701 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.701 | |
| 2jcx | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.701 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.701 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.700 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.700 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.700 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.699 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.699 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.698 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.698 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.696 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.695 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.695 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.695 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.695 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.694 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.693 | |
| 3zhb | NAP | Putative dehydrogenase | / | 0.693 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.691 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.691 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.689 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.689 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.689 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.688 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.687 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.687 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.686 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.686 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.686 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.685 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.685 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.685 | |
| 4clo | NAP | Pteridine reductase | / | 0.684 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.684 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.683 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.683 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.683 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.682 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.682 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.681 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.681 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.681 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.681 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.681 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.681 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.680 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.680 | |
| 3ras | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.680 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.680 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.680 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.679 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.679 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.679 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.679 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.679 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.678 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.678 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.677 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.677 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.676 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.676 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.675 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.674 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.674 | |
| 4kwh | NAP | Reductase homolog | / | 0.674 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.673 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.673 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.672 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.672 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.671 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.670 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.670 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.670 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.669 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.669 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.668 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.668 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.668 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.668 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.668 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.667 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.667 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.667 | |
| 4fda | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.667 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.666 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.666 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.666 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.666 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.664 | |
| 3bmo | NAP | Pteridine reductase | / | 0.663 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.663 | |
| 5aq1 | NDP | Glucose-6-phosphate 1-dehydrogenase | / | 0.663 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.662 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.662 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.662 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.661 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.661 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.661 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.660 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.660 | |
| 3e8x | NAP | BH1520 protein | / | 0.659 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.659 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.659 | |
| 4ccq | NAP | Thioredoxin reductase | / | 0.659 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.658 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.658 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.658 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.658 | |
| 3i6q | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.658 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.657 | |
| 3au2 | DGT | DNA polymerase beta family (X family) | / | 0.657 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.657 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.657 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.656 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.656 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.655 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.655 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.654 | |
| 2wow | NDP | Trypanothione reductase | / | 0.654 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.653 | |
| 3c1o | NAP | Eugenol synthase | / | 0.653 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.653 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.653 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.652 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.652 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.652 | |
| 4weq | NAP | NAD-dependent dehydrogenase | / | 0.652 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.651 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.650 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.650 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.650 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.650 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.650 |