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 |
|---|---|---|---|
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 1.370 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 1.116 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 1.005 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 1.004 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.996 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.987 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.974 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.971 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.963 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.943 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.936 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.934 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.917 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.910 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.907 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.904 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.886 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.876 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.872 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.860 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.854 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.842 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.833 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.825 | |
| 5d2e | NAP | MlnE | / | 0.813 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.811 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.807 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.795 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.789 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.785 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.780 | |
| 3mje | NDP | AmphB | / | 0.770 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.770 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.768 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.759 | |
| 3bmo | NAP | Pteridine reductase | / | 0.756 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.749 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.748 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.747 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.744 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.743 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.741 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.740 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.740 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.738 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.738 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.737 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.737 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.736 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.735 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.733 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.732 | |
| 4clo | NAP | Pteridine reductase | / | 0.730 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.729 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.729 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.729 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.726 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.725 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.725 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.724 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.724 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.724 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.723 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.723 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.723 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.723 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.719 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.718 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.716 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.716 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.714 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.713 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.712 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.712 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.712 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.712 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.712 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.710 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.710 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.710 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.710 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.709 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.707 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.707 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.706 | |
| 4u7w | NDP | MxaA | / | 0.705 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.704 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.704 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.703 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.700 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.700 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.700 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.699 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.698 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.698 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.698 | |
| 4hxy | NDP | Plm1 | / | 0.698 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.697 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.696 | |
| 4qec | NAP | ElxO | / | 0.696 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.695 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.695 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.693 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.692 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.692 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.692 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.692 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.691 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.691 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.691 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.691 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.690 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.689 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.689 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.688 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.688 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.688 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.687 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.687 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.687 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.687 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.687 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.686 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.686 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.686 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.686 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.686 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.684 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.684 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.683 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.683 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.683 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.683 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.682 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.682 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.682 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.681 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.681 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.680 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.679 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.678 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.677 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.676 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.676 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.676 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.676 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.675 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.675 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.674 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.673 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.673 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.673 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.673 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.672 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.672 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.671 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.670 | |
| 4c5o | FAD | Putative monooxygenase | / | 0.670 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.670 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.669 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.669 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.669 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.669 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.668 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.668 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.668 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.668 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.668 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.668 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.668 | |
| 4qed | NAP | ElxO | / | 0.668 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.668 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.667 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.667 | |
| 2p9e | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.666 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.666 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.666 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.666 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.666 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.665 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.665 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.664 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.664 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.664 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.664 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.664 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.664 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.663 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.661 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.661 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.661 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.661 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.660 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.660 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.660 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.659 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.659 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.657 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.656 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.656 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.656 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.656 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.656 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.656 | |
| 1h6a | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.655 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.655 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.655 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.655 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.654 | |
| 1iy8 | NAD | Levodione reductase | / | 0.653 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.653 | |
| 1h6b | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.652 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.650 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.650 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.650 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.650 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.650 |