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 |
|---|---|---|---|
| 3uce | NDP | Dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3uce | NDP | Dehydrogenase | / | 1.373 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.905 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.880 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.859 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.859 | |
| 5d2e | NAP | MlnE | / | 0.859 | |
| 4hxy | NDP | Plm1 | / | 0.841 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.838 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.837 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.836 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.836 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.830 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.830 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.830 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.823 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.822 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.814 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.814 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.811 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.809 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.807 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.807 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.804 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.804 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.800 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.799 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.798 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.790 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.788 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.785 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.785 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.784 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.784 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.783 | |
| 4kwh | NAP | Reductase homolog | / | 0.781 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.779 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.778 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.776 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.770 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.770 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.769 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.769 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.766 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.766 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.764 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.764 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.764 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.762 | |
| 3sju | NDP | Keto reductase | / | 0.762 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.762 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.761 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.761 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.759 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.759 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.757 | |
| 4u7w | NDP | MxaA | / | 0.757 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.754 | |
| 3mje | NDP | AmphB | / | 0.754 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.753 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.753 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.752 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.751 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.751 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.751 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.750 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.750 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.748 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.748 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.747 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.746 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.745 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.745 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.744 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.744 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.744 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.743 | |
| 1sny | NAP | LD36273p | / | 0.743 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.742 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.740 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.739 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.738 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.736 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.735 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.734 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.733 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.732 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.732 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.731 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.729 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.729 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.729 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.728 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.727 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.727 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.727 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.726 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.724 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.723 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.722 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.721 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.720 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.719 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.717 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.717 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.717 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.717 | |
| 4qed | NAP | ElxO | / | 0.717 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.716 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.715 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.714 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.714 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.714 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.714 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.712 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.712 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.711 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.711 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.711 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.711 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.710 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.710 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.710 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.708 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.708 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.706 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.706 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.706 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.705 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.705 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.705 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.704 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.703 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.702 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.702 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.702 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.701 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.700 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.699 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.699 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.698 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.697 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.697 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.697 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.696 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.696 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.695 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.695 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.695 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.695 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.694 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.694 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.693 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.693 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.693 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.693 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.693 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.691 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.690 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.690 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.690 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.688 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.688 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.688 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.687 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.687 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.687 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.687 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.686 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.686 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.685 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.685 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.684 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.684 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.683 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.683 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.683 | |
| 4qec | NAP | ElxO | / | 0.683 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.682 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.681 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.681 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.680 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.679 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.677 | |
| 2yjz | NAP | Metalloreductase STEAP4 | 1.16.1 | 0.677 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.676 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.675 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.675 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.675 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.674 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.673 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.673 | |
| 5aq1 | NDP | Glucose-6-phosphate 1-dehydrogenase | / | 0.673 | |
| 1iy8 | NAD | Levodione reductase | / | 0.672 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.671 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.671 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.667 | |
| 2x1e | X1E | Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form | 2.3.1.164 | 0.666 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.665 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.664 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.663 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.663 | |
| 1evj | NAD | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.661 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.661 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.660 | |
| 1e7y | NDP | Glucose-6-phosphate 1-dehydrogenase | / | 0.658 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.658 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.658 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.657 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.657 | |
| 4ocg | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.657 | |
| 2q0l | NAP | Thioredoxin reductase | 1.8.1.9 | 0.656 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.656 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.656 | |
| 4l4x | NDP | AmphI | / | 0.656 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.655 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.654 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.654 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.653 | |
| 4fda | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.653 | |
| 3i6i | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.652 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.650 |