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 |
|---|---|---|---|
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 1.450 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 1.167 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 1.125 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 1.035 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.905 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.899 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.866 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.852 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.845 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.841 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.840 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.832 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.829 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.828 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.826 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.818 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.814 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.814 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.813 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.807 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.798 | |
| 5d2e | NAP | MlnE | / | 0.797 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.794 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.793 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.792 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.790 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.790 | |
| 3mje | NDP | AmphB | / | 0.789 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.784 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.781 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.781 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.777 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.766 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.766 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.765 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.765 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.762 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.761 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.760 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.759 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.754 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.753 | |
| 4u7w | NDP | MxaA | / | 0.753 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.751 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.751 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.751 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.749 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.748 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.747 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.744 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.743 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.743 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.742 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.739 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.739 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.739 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.738 | |
| 4hxy | NDP | Plm1 | / | 0.738 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.737 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.737 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.736 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.734 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.731 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.730 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.730 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.729 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.728 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.728 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.726 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.726 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.726 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.726 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.725 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.725 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.724 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.723 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.722 | |
| 4clo | NAP | Pteridine reductase | / | 0.722 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.721 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.720 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.720 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.719 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.719 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.719 | |
| 1sny | NAP | LD36273p | / | 0.718 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.717 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.717 | |
| 4kwh | NAP | Reductase homolog | / | 0.717 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.716 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.715 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.712 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.711 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.711 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.710 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.710 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.710 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.709 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.709 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.707 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.707 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.707 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.707 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.706 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.706 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.706 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.706 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.705 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.705 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.704 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.704 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.704 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.703 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.702 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.702 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.701 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.700 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.700 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.700 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.699 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.699 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.698 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.695 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.695 | |
| 3uce | NDP | Dehydrogenase | / | 0.695 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.695 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.695 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.695 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.693 | |
| 3sju | NDP | Keto reductase | / | 0.693 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.692 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.691 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.691 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.690 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.689 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.689 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.689 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.689 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.688 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.686 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.686 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.686 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.683 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.682 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.682 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.681 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.681 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.681 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.680 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.679 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.678 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.678 | |
| 1zh8 | NAP | Uncharacterized protein | / | 0.677 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.677 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.677 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.675 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.675 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.675 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.674 | |
| 3oa2 | NAD | UDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase | / | 0.674 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.674 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.673 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.673 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.673 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.673 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.673 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.673 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.672 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.672 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.671 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.670 | |
| 2ixb | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.670 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.670 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.670 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.668 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.667 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.667 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.667 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.667 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.664 | |
| 1u7h | NAD | Putative ornithine cyclodeaminase | / | 0.663 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.663 | |
| 1h6a | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.662 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.662 | |
| 1x7d | NAD | Putative ornithine cyclodeaminase | / | 0.661 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.661 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.661 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.661 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.661 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.660 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.660 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.659 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.659 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.659 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.659 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.658 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.658 | |
| 4qed | NAP | ElxO | / | 0.657 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.656 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.656 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.655 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.655 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.655 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.654 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.653 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.653 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.652 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.652 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.651 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.651 | |
| 4e5m | NAP | Phosphonate dehydrogenase | 1.20.1.1 | 0.651 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.650 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.650 |