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 |
|---|---|---|---|
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 1.310 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.935 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.900 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.878 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.872 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.860 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.856 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.848 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.845 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.844 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.833 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.820 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.820 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.819 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.816 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.814 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.813 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.810 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.807 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.805 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.801 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.798 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.796 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.793 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.792 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.791 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.788 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.783 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.780 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.776 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.775 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.771 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.769 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.768 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.768 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.766 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.766 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.763 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.763 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.762 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.761 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.759 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.758 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.757 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.757 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.756 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.756 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.755 | |
| 4qed | NAP | ElxO | / | 0.755 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.754 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.753 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.751 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.751 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.751 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.750 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.749 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.749 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.749 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.748 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.747 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.746 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.745 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.744 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.744 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.744 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.744 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.743 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.742 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.741 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.738 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.737 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.735 | |
| 3sju | NDP | Keto reductase | / | 0.735 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.734 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.732 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.732 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.729 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.728 | |
| 4kwh | NAP | Reductase homolog | / | 0.728 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.727 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.727 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.727 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.726 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.726 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.725 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.721 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.720 | |
| 1iy8 | NAD | Levodione reductase | / | 0.720 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.720 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.717 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.717 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.717 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.715 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.712 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.712 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.711 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.710 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.709 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.708 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.708 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.708 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.706 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.705 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.705 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.704 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.704 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.703 | |
| 2ztu | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.703 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.702 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.700 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.699 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.699 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.699 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.698 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.695 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.695 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.695 | |
| 5je2 | SAH | Methyl transferase | / | 0.693 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.692 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.692 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.691 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.689 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.688 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.688 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.688 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.688 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.688 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.687 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.687 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.686 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.686 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.686 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.685 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.685 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.685 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.684 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.684 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.681 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.681 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.681 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.679 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.679 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.678 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.678 | |
| 3mje | NDP | AmphB | / | 0.677 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.676 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.676 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.674 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.674 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.673 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.673 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.673 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.673 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.672 | |
| 5jdz | SAH | Methyl transferase | / | 0.672 | |
| 5je3 | SAH | Methyl transferase | / | 0.672 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.671 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.670 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.668 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.668 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.668 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.666 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.666 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.666 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.666 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.665 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.665 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.663 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.663 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.661 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.661 | |
| 3lhd | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.661 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.660 | |
| 4bii | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.660 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.659 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.658 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.658 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.658 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.658 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.657 | |
| 4bgi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.657 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.657 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.657 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.657 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.656 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.656 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.655 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.655 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.654 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.654 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.654 | |
| 5d2e | NAP | MlnE | / | 0.654 | |
| 4hxy | NDP | Plm1 | / | 0.653 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.652 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.652 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.651 | |
| 1nvm | NAD | Acetaldehyde dehydrogenase | 1.2.1.10 | 0.651 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.651 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.651 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.651 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.651 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.650 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.650 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.650 |