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 |
|---|---|---|---|
| 3a4v | NAD | NDP-sugar epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3a4v | NAD | NDP-sugar epimerase | / | 1.127 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.953 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.919 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.877 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.853 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.827 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.788 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.786 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.783 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.783 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.774 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.771 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.764 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.763 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.762 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.760 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.760 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.754 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.753 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.752 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.751 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.750 | |
| 4hxy | NDP | Plm1 | / | 0.745 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.744 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.742 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.741 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.741 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.740 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.737 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.734 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.734 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.734 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.730 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.730 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.730 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.729 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.729 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.729 | |
| 4kwh | NAP | Reductase homolog | / | 0.728 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.725 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.724 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.721 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.721 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.720 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.720 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.720 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.720 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.719 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.717 | |
| 4qec | NAP | ElxO | / | 0.717 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.716 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.715 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.715 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.715 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.714 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.714 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.713 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.712 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.711 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.711 | |
| 4qed | NAP | ElxO | / | 0.711 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.710 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.709 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.709 | |
| 4ros | APR | Malate dehydrogenase | / | 0.709 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.708 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.707 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.707 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.707 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.707 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.706 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.705 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.705 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.705 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.704 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.702 | |
| 4u7w | NDP | MxaA | / | 0.702 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.701 | |
| 3mje | NDP | AmphB | / | 0.701 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.701 | |
| 3uce | NDP | Dehydrogenase | / | 0.701 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.700 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.699 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.699 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.699 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.698 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.698 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.697 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.696 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.696 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.695 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.695 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.694 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.694 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.694 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.693 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.692 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.690 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.689 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.688 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.688 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.688 | |
| 3sju | NDP | Keto reductase | / | 0.685 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.685 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.684 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.684 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.684 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.684 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.684 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.684 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.684 | |
| 5d2e | NAP | MlnE | / | 0.684 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.683 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.682 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.682 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.682 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.682 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.681 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.680 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.680 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.680 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.679 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.679 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.679 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.678 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.678 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.678 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.677 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.677 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.677 | |
| 1sc6 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.676 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.675 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.675 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.675 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.674 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.674 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.674 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.674 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.674 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.673 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.673 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.673 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.673 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.672 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.672 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.672 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.671 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.671 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.671 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.671 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.670 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.670 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.670 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.670 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.669 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.669 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.668 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.668 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.668 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.667 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.667 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.667 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.667 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.666 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.666 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.665 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.665 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.664 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.663 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.662 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.661 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.661 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.660 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.660 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.660 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.659 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.658 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.658 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.658 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.657 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.657 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.657 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.656 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.656 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.655 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.655 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.655 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.654 | |
| 4k9d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.654 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.654 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.653 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.653 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.653 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.652 | |
| 4clo | NAP | Pteridine reductase | / | 0.652 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.652 | |
| 1dss | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.651 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.651 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.651 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.651 | |
| 4l4x | NDP | AmphI | / | 0.651 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.651 | |
| 3bmo | NAP | Pteridine reductase | / | 0.650 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.650 |