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 |
|---|---|---|---|
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 1.042 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.883 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.876 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.875 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.866 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.858 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.844 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.840 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.803 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.790 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.788 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.776 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.761 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.759 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.759 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.758 | |
| 3mje | NDP | AmphB | / | 0.754 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.752 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.752 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.751 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.751 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.750 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.748 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.746 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.746 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.744 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.743 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.741 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.739 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.736 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.735 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.735 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.735 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.734 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.733 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.732 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.731 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.731 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.729 | |
| 4hxy | NDP | Plm1 | / | 0.729 | |
| 4kwh | NAP | Reductase homolog | / | 0.727 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.725 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.725 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.724 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.723 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.722 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.720 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.718 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.718 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.715 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.715 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.714 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.714 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.714 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.714 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.713 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.713 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.713 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.713 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.712 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.711 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.710 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.710 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.709 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.709 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.707 | |
| 4u7w | NDP | MxaA | / | 0.707 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.706 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.706 | |
| 4qec | NAP | ElxO | / | 0.706 | |
| 5d2e | NAP | MlnE | / | 0.705 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.704 | |
| 4qed | NAP | ElxO | / | 0.704 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.701 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.701 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.700 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.699 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.698 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.698 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.697 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.697 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.697 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.696 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.696 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.696 | |
| 1iy8 | NAD | Levodione reductase | / | 0.695 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.695 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.695 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.694 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.694 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.694 | |
| 4clo | NAP | Pteridine reductase | / | 0.693 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.693 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.693 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.692 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.692 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.691 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.691 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.691 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.690 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.689 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.689 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.689 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.688 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.687 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.687 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.687 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.687 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.686 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.685 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.684 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.684 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.683 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.683 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.682 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.681 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.681 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.681 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.680 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.680 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.680 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.680 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.679 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.679 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.678 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.677 | |
| 3sju | NDP | Keto reductase | / | 0.677 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.676 | |
| 3bmo | NAP | Pteridine reductase | / | 0.676 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.676 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.675 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.675 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.675 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.674 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.674 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.674 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.674 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.673 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.672 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.672 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.672 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.672 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.670 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.670 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.670 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.670 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.669 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.669 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.669 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.668 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.668 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.668 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.668 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.668 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.667 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.667 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.667 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.667 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.666 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.664 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.664 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.662 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.662 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.661 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.660 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.660 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.660 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.660 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.660 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.659 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.659 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.659 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.659 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.659 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.658 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.658 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.658 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.658 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.657 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.657 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.656 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.656 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.656 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.656 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.655 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.655 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.654 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.654 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.653 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.653 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.653 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.651 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.651 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.650 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 |