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 |
|---|---|---|---|
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 1.288 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.972 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.855 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.808 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.796 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.788 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.787 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.781 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.778 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.770 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.769 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.760 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.757 | |
| 4u7w | NDP | MxaA | / | 0.757 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.742 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.742 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.740 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.739 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.735 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.732 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.731 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.730 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.729 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.728 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.727 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.725 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.724 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.723 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.723 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.722 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.722 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.720 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.720 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.720 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.719 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.719 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.719 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.718 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.718 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.717 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.716 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.715 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.715 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.715 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.715 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.715 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.714 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.714 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.712 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.712 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.707 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.707 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.706 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.705 | |
| 4gae | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.704 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.703 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.701 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.700 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.700 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.700 | |
| 4kwh | NAP | Reductase homolog | / | 0.700 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.700 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.700 | |
| 3oa2 | NAD | UDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase | / | 0.698 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.698 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.696 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.696 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.696 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.696 | |
| 4hxy | NDP | Plm1 | / | 0.696 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.695 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.695 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.695 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.695 | |
| 4aic | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.695 | |
| 1il0 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.694 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.694 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.694 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.694 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.693 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.693 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.693 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.692 | |
| 4clo | NAP | Pteridine reductase | / | 0.692 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.692 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.691 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.691 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.691 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.690 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.690 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.690 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.690 | |
| 5a06 | NDP | Glucose-fructose oxidoreductase | / | 0.690 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.689 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.689 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.689 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.688 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.687 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.687 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.686 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.685 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.685 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.685 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.685 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.684 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.684 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.684 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.683 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.683 | |
| 4qec | NAP | ElxO | / | 0.683 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.683 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.682 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.682 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.681 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.681 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.680 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.680 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.680 | |
| 3ras | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.680 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.680 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.679 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.679 | |
| 2ixa | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.678 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.678 | |
| 2ixb | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.677 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.677 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.676 | |
| 1sny | NAP | LD36273p | / | 0.676 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.676 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.676 | |
| 3uce | NDP | Dehydrogenase | / | 0.676 | |
| 4l4x | NDP | AmphI | / | 0.676 | |
| 5d2e | NAP | MlnE | / | 0.676 | |
| 1f0y | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.675 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.675 | |
| 2jd1 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.675 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.675 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.675 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.675 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.673 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.673 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.673 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.673 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.673 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.672 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.672 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.672 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.672 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.671 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.670 | |
| 1iy8 | NAD | Levodione reductase | / | 0.670 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.670 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.670 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.669 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.669 | |
| 3mje | NDP | AmphB | / | 0.669 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.668 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.668 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.668 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.668 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.667 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.667 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.666 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.666 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.666 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.666 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.665 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.665 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.664 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.664 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.664 | |
| 3bmo | NAP | Pteridine reductase | / | 0.664 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.663 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.663 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.663 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.663 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.662 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.662 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.662 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.662 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.662 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.660 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.659 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.659 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.659 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.658 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.658 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.658 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.657 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.657 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.657 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.657 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.657 | |
| 6adh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.657 | |
| 3i6q | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.656 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.656 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.656 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.655 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.655 | |
| 3pdu | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.655 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.655 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.654 | |
| 3i6i | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.654 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.653 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.652 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.652 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.651 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.651 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.651 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.651 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.651 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.650 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 |