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 |
|---|---|---|---|
| 3a9w | NAD | NDP-sugar epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3a9w | NAD | NDP-sugar epimerase | / | 1.128 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 1.033 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.919 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.841 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.809 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.803 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.792 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.785 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.777 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.770 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.759 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.752 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.750 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.746 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.745 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.744 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.741 | |
| 4u7w | NDP | MxaA | / | 0.740 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.738 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.738 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.737 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.737 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.737 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.736 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.735 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.734 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.733 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.731 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.731 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.730 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.729 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.728 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.728 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.727 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.726 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.726 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.725 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.725 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.724 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.722 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.721 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.721 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.718 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.718 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.715 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.715 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.714 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.714 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.713 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.711 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.710 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.710 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.707 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.706 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.705 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.705 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.705 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.705 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.704 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.704 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.703 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.703 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.702 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.702 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.702 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.700 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.700 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.700 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.700 | |
| 4qec | NAP | ElxO | / | 0.700 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.699 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.699 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.699 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.699 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.699 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.698 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.698 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.697 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.695 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.695 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.695 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.695 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.694 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.694 | |
| 1iy8 | NAD | Levodione reductase | / | 0.693 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.693 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.693 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.692 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.692 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.692 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.692 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.692 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.692 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.691 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.691 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.690 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.688 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.688 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.687 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.687 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.686 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.685 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.685 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.685 | |
| 4qed | NAP | ElxO | / | 0.685 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.684 | |
| 3mje | NDP | AmphB | / | 0.684 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.684 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.683 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.683 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.683 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.682 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.682 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.681 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.681 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.680 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.680 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.679 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.678 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.678 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.678 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.678 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.677 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.677 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.677 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.677 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.677 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.675 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.675 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.675 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.674 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.674 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.673 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.673 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.672 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.672 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.672 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.672 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.672 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.671 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.671 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.671 | |
| 4kwh | NAP | Reductase homolog | / | 0.671 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.670 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.670 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.670 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.669 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.669 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.669 | |
| 5d2e | NAP | MlnE | / | 0.669 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.668 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.668 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.668 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.667 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.666 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.666 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.665 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.665 | |
| 4l4x | NDP | AmphI | / | 0.665 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.664 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.664 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.664 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.663 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.663 | |
| 1cf2 | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.662 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.662 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.661 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.661 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.661 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.660 | |
| 1i36 | NAP | Conserved protein | / | 0.660 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.660 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.660 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.660 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.658 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.658 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.657 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.657 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.657 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.657 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.657 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.657 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.656 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.656 | |
| 1pnq | NDP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.654 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.654 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.653 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.653 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.653 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.653 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.653 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.652 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.651 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.651 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.651 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.650 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.650 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.650 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.650 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.650 |