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 |
|---|---|---|---|
| 1rpn | NDP | GDP-mannose 4,6-dehydratase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 1.403 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 1.017 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 1.006 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.996 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.910 | |
| 3mje | NDP | AmphB | / | 0.813 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.780 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.779 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.779 | |
| 3uce | NDP | Dehydrogenase | / | 0.778 | |
| 4u7w | NDP | MxaA | / | 0.773 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.772 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.771 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.766 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.765 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.764 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.761 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.760 | |
| 5d2e | NAP | MlnE | / | 0.760 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.756 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.755 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.755 | |
| 4hxy | NDP | Plm1 | / | 0.751 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.750 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.748 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.748 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.741 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.739 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.738 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.737 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.736 | |
| 4clo | NAP | Pteridine reductase | / | 0.736 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.732 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.730 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.730 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.730 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.729 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.727 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.726 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.726 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.726 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.724 | |
| 1sny | NAP | LD36273p | / | 0.724 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.724 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.724 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.723 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.718 | |
| 3sju | NDP | Keto reductase | / | 0.718 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.717 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.717 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.717 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.715 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.712 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.712 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.711 | |
| 3bmo | NAP | Pteridine reductase | / | 0.709 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.709 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.708 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.708 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.707 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.706 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.706 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.701 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.701 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.700 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.698 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.697 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.696 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.695 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.694 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.693 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.693 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.693 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.693 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.692 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.692 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.691 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.691 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.691 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.691 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.689 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.686 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.685 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.685 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.685 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.683 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.683 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.682 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.682 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.682 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.682 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.682 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.681 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.681 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.681 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.681 | |
| 4qed | NAP | ElxO | / | 0.681 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.680 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.680 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.680 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.680 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.680 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.680 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.679 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.679 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.679 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.678 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.677 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.677 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.676 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.676 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.676 | |
| 3up5 | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.675 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.675 | |
| 4l4x | NDP | AmphI | / | 0.675 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.675 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.673 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.673 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.673 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.673 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.672 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.671 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.671 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.670 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.670 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.670 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.669 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.669 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.669 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.669 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.669 | |
| 3pdu | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.668 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.668 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.667 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.667 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.667 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.667 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.667 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.667 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.666 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.666 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.666 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.665 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.665 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.664 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.663 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.663 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.662 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.662 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.662 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.661 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.661 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.661 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.659 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.659 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.657 | |
| 2wzm | NA7 | Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346 | / | 0.657 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.656 | |
| 1iy8 | NAD | Levodione reductase | / | 0.655 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.655 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.655 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.653 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.653 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.653 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.653 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.653 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.653 | |
| 4kwh | NAP | Reductase homolog | / | 0.652 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.651 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.650 | |
| 1w35 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.650 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.650 |