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 |
|---|---|---|---|
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 1.373 | |
| 4hxy | NDP | Plm1 | / | 0.857 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.841 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.825 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.802 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.789 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.788 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.788 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.787 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.786 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.779 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.775 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.774 | |
| 5d2e | NAP | MlnE | / | 0.773 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.772 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.772 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.771 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.769 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.766 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.766 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.765 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.763 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.763 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.761 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.759 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.758 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.756 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.756 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.754 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.754 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.752 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.752 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.751 | |
| 3mje | NDP | AmphB | / | 0.748 | |
| 3uce | NDP | Dehydrogenase | / | 0.748 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.746 | |
| 1w73 | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.745 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.743 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.742 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.742 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.740 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.739 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.737 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.737 | |
| 3sju | NDP | Keto reductase | / | 0.737 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.736 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.735 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.733 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.733 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.729 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.728 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.728 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.726 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.726 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.725 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.724 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.724 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.724 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.724 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.723 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.723 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.723 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.722 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.722 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.719 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.717 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.716 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.716 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.715 | |
| 3baz | NAP | Hydroxyphenylpyruvate reductase | 1.1.1.237 | 0.714 | |
| 4clo | NAP | Pteridine reductase | / | 0.713 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.711 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.710 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.709 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.708 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.707 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.707 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.705 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.705 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.705 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.704 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.702 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.701 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.699 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.699 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.698 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.697 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.696 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.696 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.694 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.693 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.693 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.692 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.692 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.690 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.689 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.689 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.688 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.688 | |
| 1pt9 | TAP | NAD(P) transhydrogenase, mitochondrial | 1.6.1.2 | 0.685 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.685 | |
| 2dt5 | NAD | Redox-sensing transcriptional repressor Rex | / | 0.683 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.682 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.680 | |
| 1d4o | NAP | NAD(P) transhydrogenase, mitochondrial | / | 0.679 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.679 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.678 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.678 | |
| 3iup | NDP | Possible NADH oxidoreductase | / | 0.678 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.677 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.677 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.677 | |
| 4u7w | NDP | MxaA | / | 0.677 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.677 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.676 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.676 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.675 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.675 | |
| 4qec | NAP | ElxO | / | 0.675 | |
| 2vwh | NAP | Glucose 1-dehydrogenase | / | 0.674 | |
| 4l4x | NDP | AmphI | / | 0.674 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.674 | |
| 1iy8 | NAD | Levodione reductase | / | 0.672 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.672 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.672 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.671 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.671 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.670 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.670 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.669 | |
| 1sny | NAP | LD36273p | / | 0.669 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.669 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.667 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.667 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.667 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.666 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.666 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.665 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.665 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.664 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.663 | |
| 3ntd | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.663 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.663 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.662 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.661 | |
| 4qed | NAP | ElxO | / | 0.661 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.660 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.660 | |
| 3bmo | NAP | Pteridine reductase | / | 0.660 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.660 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.659 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.658 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.658 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.658 | |
| 1djl | NAP | NAD(P) transhydrogenase, mitochondrial | 1.6.1.2 | 0.657 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.657 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.657 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.657 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.657 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.655 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.655 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.655 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.654 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.654 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.654 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.654 | |
| 1ht0 | NAD | Alcohol dehydrogenase 1C | 1.1.1.1 | 0.653 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.653 | |
| 1u31 | NDP | NAD(P) transhydrogenase, mitochondrial | 1.6.1.2 | 0.653 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.653 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.653 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.653 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.652 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.652 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.652 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.651 | |
| 1ptj | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.651 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.651 | |
| 5a03 | NDP | Glucose-fructose oxidoreductase | / | 0.651 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.651 | |
| 1evj | NAD | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.650 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.650 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.650 |