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 |
|---|---|---|---|
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 1.233 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.998 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.994 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.990 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.945 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.926 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.912 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.910 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.900 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.896 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.892 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.892 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.889 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.884 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.882 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.875 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.869 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.869 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.863 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.855 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.845 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.844 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.841 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.840 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.839 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.839 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.837 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.832 | |
| 4u7w | NDP | MxaA | / | 0.825 | |
| 5d2e | NAP | MlnE | / | 0.817 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.816 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.811 | |
| 4hxy | NDP | Plm1 | / | 0.811 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.809 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.800 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.799 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.797 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.795 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.793 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.793 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.789 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.786 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.786 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.785 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.784 | |
| 3bmo | NAP | Pteridine reductase | / | 0.781 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.780 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.778 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.776 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.772 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.771 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.769 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.769 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.766 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.762 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.761 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.758 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.757 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.756 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.754 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.752 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.751 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.749 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.747 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.746 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.746 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.746 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.744 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.744 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.743 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.741 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.741 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.741 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.740 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.740 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.739 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.739 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.739 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.738 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.738 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.737 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.736 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.735 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.734 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.734 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.732 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.731 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.731 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.731 | |
| 4kwh | NAP | Reductase homolog | / | 0.729 | |
| 4qec | NAP | ElxO | / | 0.729 | |
| 4clo | NAP | Pteridine reductase | / | 0.727 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.726 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.726 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.724 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.724 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.724 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.723 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.722 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.722 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.721 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.721 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.720 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.719 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.719 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.719 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.717 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.716 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.716 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.714 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.714 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.714 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.711 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.711 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.709 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.709 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.709 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.709 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.709 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.709 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.709 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.705 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.704 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.704 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.704 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.703 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.703 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.701 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.701 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.701 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.700 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.699 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.698 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.698 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.697 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.696 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.696 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.696 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.695 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.694 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.694 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.693 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.693 | |
| 3uce | NDP | Dehydrogenase | / | 0.693 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.693 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.692 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.692 | |
| 3m2t | NAD | Probable dehydrogenase | / | 0.690 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.690 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.689 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.688 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.688 | |
| 4l4x | NDP | AmphI | / | 0.688 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.685 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.684 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.682 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.682 | |
| 1zh8 | NAP | Uncharacterized protein | / | 0.681 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.681 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.681 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.680 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.680 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.680 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.679 | |
| 1iy8 | NAD | Levodione reductase | / | 0.678 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.678 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.678 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.677 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.677 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.675 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.675 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.673 | |
| 3q2k | NAI | Probable oxidoreductase | / | 0.673 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.673 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.673 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.671 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.669 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.669 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.669 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.668 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.668 | |
| 4qed | NAP | ElxO | / | 0.668 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.667 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.665 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.663 | |
| 3mje | NDP | AmphB | / | 0.663 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.662 | |
| 1j5p | NAD | L-aspartate dehydrogenase | 1.4.1.21 | 0.661 | |
| 4ros | APR | Malate dehydrogenase | / | 0.661 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.660 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.660 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.660 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.660 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.658 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.658 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.658 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.657 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.657 | |
| 3i6i | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.657 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.657 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.656 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.656 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.656 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.656 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.656 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.655 | |
| 3adp | NAI | Lambda-crystallin | 1.1.1.45 | 0.655 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.655 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.655 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.655 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.654 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.654 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.654 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.654 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.653 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.653 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.652 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.651 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.651 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.651 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.651 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.650 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.650 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.650 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.650 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.650 |