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 |
|---|---|---|---|
| 2p5u | NAD | UDP-glucose 4-epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 1.257 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 1.064 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.915 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.885 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.877 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.864 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.855 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.845 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.841 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.841 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.837 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.834 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.832 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.828 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.826 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.822 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.820 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.819 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.816 | |
| 4qec | NAP | ElxO | / | 0.811 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.803 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.802 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.801 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.800 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.798 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.795 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.781 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.780 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.779 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.778 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.777 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.771 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.769 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.768 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.766 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.765 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.760 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.760 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.757 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.757 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.757 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.755 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.753 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.750 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.747 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.747 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.746 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.746 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.746 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.745 | |
| 4qed | NAP | ElxO | / | 0.745 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.744 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.744 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.744 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.743 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.743 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.743 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.741 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.739 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.739 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.738 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.738 | |
| 4u7w | NDP | MxaA | / | 0.737 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.736 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.735 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.734 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.733 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.733 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.731 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.731 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.730 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.730 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.729 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.729 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.722 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.722 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.722 | |
| 3mje | NDP | AmphB | / | 0.721 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.720 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.718 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.718 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.718 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.717 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.716 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.716 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.714 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.714 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.714 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.712 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.712 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.711 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.709 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.709 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.707 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.706 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.703 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.702 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.702 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.702 | |
| 4hxy | NDP | Plm1 | / | 0.701 | |
| 4kwh | NAP | Reductase homolog | / | 0.701 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.699 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.699 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.697 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.697 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.697 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.697 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.697 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.696 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.696 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.696 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.695 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.695 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.694 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.693 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.692 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.692 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.692 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.692 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.691 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.691 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.690 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.690 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.689 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.688 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.688 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.687 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.687 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.686 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.686 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.686 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.685 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.684 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.683 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.683 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.682 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.681 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.680 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.680 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.680 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.679 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.679 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.679 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.679 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.678 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.678 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.678 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.678 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.678 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.677 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.677 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.676 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.676 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.675 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.674 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.674 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.674 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.674 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.674 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.674 | |
| 1sny | NAP | LD36273p | / | 0.672 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.672 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.670 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.670 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.669 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.669 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.668 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.668 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.668 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.667 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.666 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.666 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.665 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.665 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.665 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.665 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.665 | |
| 4l4x | NDP | AmphI | / | 0.665 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.664 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.664 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.663 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.662 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.660 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.660 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.660 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.660 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.660 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.659 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.658 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.658 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.658 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.658 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.658 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.657 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.657 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.657 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.656 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.656 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.656 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.656 | |
| 5d2e | NAP | MlnE | / | 0.656 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.655 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.655 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.655 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.655 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.655 | |
| 3bmo | NAP | Pteridine reductase | / | 0.654 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.654 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.652 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.651 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.651 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.651 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.651 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.650 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.650 |