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 |
|---|---|---|---|
| 3pdu | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3pdu | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 1.460 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 1.238 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.964 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.942 | |
| 1wp4 | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.904 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.899 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.798 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.795 | |
| 2i9p | NAD | 3-hydroxyisobutyrate dehydrogenase, mitochondrial | 1.1.1.31 | 0.793 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.779 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.772 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.764 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.756 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.753 | |
| 3abi | NAD | Uncharacterized protein | / | 0.746 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.742 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.742 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.741 | |
| 4xb2 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.740 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.737 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.735 | |
| 1q0q | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.735 | |
| 1u7h | NAD | Putative ornithine cyclodeaminase | / | 0.733 | |
| 1i36 | NAP | Conserved protein | / | 0.732 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.732 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.731 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.730 | |
| 1x7d | NAD | Putative ornithine cyclodeaminase | / | 0.729 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.726 | |
| 3wfj | NAD | 2-dehydropantoate 2-reductase | / | 0.726 | |
| 4plp | NAD | Homospermidine synthase | 2.5.1.44 | 0.725 | |
| 1nvm | NAD | Acetaldehyde dehydrogenase | 1.2.1.10 | 0.723 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.722 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.722 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.721 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.718 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.716 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.716 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.715 | |
| 2iyp | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.713 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.712 | |
| 3anm | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.711 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.710 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.708 | |
| 2uyy | NA7 | Putative oxidoreductase GLYR1 | 1 | 0.707 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.705 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.705 | |
| 2iyp | A2P | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.704 | |
| 3ulk | NDP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.702 | |
| 3hwr | NDP | 2-dehydropantoate 2-reductase | / | 0.701 | |
| 3kbo | NDP | Glyoxylate/hydroxypyruvate reductase A | / | 0.701 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.697 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.697 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.697 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.696 | |
| 1sny | NAP | LD36273p | / | 0.693 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.693 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.692 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.691 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.690 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.690 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.690 | |
| 3keq | NAD | Redox-sensing transcriptional repressor Rex | / | 0.690 | |
| 4xr9 | NAD | CalS8 | / | 0.690 | |
| 5a03 | NDP | Glucose-fructose oxidoreductase | / | 0.690 | |
| 5a05 | NDP | Glucose-fructose oxidoreductase | / | 0.690 | |
| 5dul | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.690 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.690 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.689 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.689 | |
| 3ing | NDP | Homoserine dehydrogenase related protein | / | 0.689 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.689 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.689 | |
| 1h6d | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.688 | |
| 3anl | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.688 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.688 | |
| 5ees | NAP | 4-hydroxy-tetrahydrodipicolinate reductase | / | 0.688 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.688 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.687 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.686 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.686 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.685 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.685 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.684 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.684 | |
| 1o6z | NAD | Malate dehydrogenase | / | 0.683 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.683 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.683 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.682 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.682 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.681 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.681 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.681 | |
| 5a04 | NDP | Glucose-fructose oxidoreductase | / | 0.681 | |
| 1a71 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.680 | |
| 2q0l | NAP | Thioredoxin reductase | 1.8.1.9 | 0.680 | |
| 4ccq | NAP | Thioredoxin reductase | / | 0.680 | |
| 4oaq | NDP | R-specific carbonyl reductase | / | 0.680 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.680 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.679 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.679 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.679 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.679 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.678 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.677 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.677 | |
| 5a02 | NAP | Glucose-fructose oxidoreductase | / | 0.677 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.676 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.675 | |
| 1zh8 | NAP | Uncharacterized protein | / | 0.675 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.675 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.675 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.675 | |
| 4nfh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.675 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.674 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.673 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.672 | |
| 1h6b | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.671 | |
| 1lld | NAD | L-lactate dehydrogenase 2 | 1.1.1.27 | 0.671 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.671 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.671 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.671 | |
| 5cdt | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.671 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.671 | |
| 4dpl | NAP | Malonyl-CoA reductase | 1.2.1.75 | 0.670 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.670 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.670 | |
| 1yl7 | NAI | 4-hydroxy-tetrahydrodipicolinate reductase | / | 0.669 | |
| 3keo | NAD | Redox-sensing transcriptional repressor Rex | / | 0.669 | |
| 4xd2 | NAI | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.669 | |
| 1h6a | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.668 | |
| 1m76 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.668 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.668 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.668 | |
| 3two | NDP | Mannitol dehydrogenase | / | 0.668 | |
| 6adh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.668 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.667 | |
| 1yjq | NAP | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.667 | |
| 2dph | NAD | Formaldehyde dismutase | / | 0.667 | |
| 5cds | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.667 | |
| 5kcp | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.667 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.667 | |
| 1axe | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.666 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.666 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.666 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.666 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.666 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.666 | |
| 4aic | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.666 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.666 | |
| 4gae | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.666 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.665 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.665 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.665 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.665 | |
| 4kwh | NAP | Reductase homolog | / | 0.665 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.664 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.664 | |
| 4u7w | NDP | MxaA | / | 0.664 | |
| 5aq1 | NDP | Glucose-6-phosphate 1-dehydrogenase | / | 0.664 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.663 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.663 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.663 | |
| 1lua | NAP | Bifunctional protein MdtA | 1.5.1.5 | 0.662 | |
| 2f1k | NAP | Prephenate dehydrogenase | / | 0.662 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.662 | |
| 3e8x | NAP | BH1520 protein | / | 0.662 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.662 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.662 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.662 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.662 | |
| 4up3 | NDP | Thioredoxin reductase | / | 0.662 | |
| 5cdg | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.662 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.661 | |
| 3cea | NAD | Myo-inositol 2-dehydrogenase-like (Promiscuous) | / | 0.661 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.661 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.661 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.660 | |
| 4y0k | NAP | AntE | / | 0.660 | |
| 3mje | NDP | AmphB | / | 0.659 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.659 | |
| 4ng5 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.659 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.658 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.658 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.658 | |
| 4eil | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.658 | |
| 4om8 | NAD | 3-hydroxybutyryl-coA dehydrogenase | / | 0.658 | |
| 5doz | NDP | JamJ | / | 0.658 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.657 | |
| 4weq | NAP | NAD-dependent dehydrogenase | / | 0.657 | |
| 1agn | NAD | Alcohol dehydrogenase class 4 mu/sigma chain | 1.1.1.1 | 0.656 | |
| 1ryd | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.656 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.656 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.656 | |
| 1kol | NAD | Glutathione-independent formaldehyde dehydrogenase | / | 0.655 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.655 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.655 | |
| 2ixa | NAD | Alpha-N-acetylgalactosaminidase | 3.2.1.49 | 0.655 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.655 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.655 | |
| 4ywj | NAD | 4-hydroxy-tetrahydrodipicolinate reductase | / | 0.655 | |
| 5kj1 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.655 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.654 | |
| 2dt5 | NAD | Redox-sensing transcriptional repressor Rex | / | 0.654 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.654 | |
| 4gcm | NAP | Thioredoxin reductase | 1.8.1.9 | 0.654 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.654 | |
| 1ofg | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.653 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.653 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.653 | |
| 4xb1 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.653 | |
| 1il0 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.652 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.652 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.651 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.651 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.651 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.651 | |
| 5kj6 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.651 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.650 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.650 |