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 |
|---|---|---|---|
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 1.301 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 1.116 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 1.024 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.970 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.962 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.954 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.945 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.941 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.931 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.917 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.916 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.914 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.912 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.910 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.901 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.893 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.883 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.882 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.881 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.868 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.850 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.842 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.831 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.824 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.822 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.811 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.811 | |
| 5d2e | NAP | MlnE | / | 0.811 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.808 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.807 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.800 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.799 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.798 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.797 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.794 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.788 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.786 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.785 | |
| 3mje | NDP | AmphB | / | 0.781 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.779 | |
| 4hxy | NDP | Plm1 | / | 0.777 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.774 | |
| 4u7w | NDP | MxaA | / | 0.773 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.771 | |
| 1rpn | NDP | GDP-mannose 4,6-dehydratase | / | 0.760 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.759 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.755 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.753 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.752 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.751 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.751 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.751 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.747 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.747 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.743 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.743 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.741 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.739 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.737 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.733 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.733 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.730 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.730 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.729 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.729 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.724 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.723 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.722 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.722 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.721 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.721 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.721 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.719 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.719 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.716 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.716 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.716 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.715 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.715 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.715 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.714 | |
| 1sny | NAP | LD36273p | / | 0.713 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.711 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.711 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.710 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.710 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.708 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.705 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.705 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.704 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.703 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.703 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.702 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.701 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.701 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.701 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.700 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.700 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.699 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.699 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.698 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.698 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.696 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.696 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.696 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.696 | |
| 1iy8 | NAD | Levodione reductase | / | 0.695 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.693 | |
| 1w8d | NAP | 2,4-dienoyl-CoA reductase, mitochondrial | 1.3.1.34 | 0.693 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.693 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.692 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.692 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.692 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.691 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.691 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.689 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.689 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.689 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.688 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.688 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.686 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.685 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.684 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.684 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.684 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.684 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.682 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.682 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.682 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.682 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.681 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.681 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.680 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.680 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.680 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.680 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.679 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.679 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.679 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.679 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.678 | |
| 3sju | NDP | Keto reductase | / | 0.678 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.677 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.676 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.675 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.674 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.674 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.674 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.674 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.673 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.673 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.672 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.672 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.672 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.672 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.672 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.672 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.671 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.671 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.670 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.670 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.670 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.669 | |
| 3qw2 | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.669 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.668 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.668 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.668 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.667 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.667 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.667 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.666 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.666 | |
| 2yw9 | NAP | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.665 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.665 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.665 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.664 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.664 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.664 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.664 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.664 | |
| 4qec | NAP | ElxO | / | 0.664 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.663 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.663 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.663 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.663 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.662 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.662 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.662 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.662 | |
| 4qed | NAP | ElxO | / | 0.662 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.662 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.661 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.660 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.660 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.660 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.660 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.660 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.660 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.659 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.659 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.658 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.657 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.657 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.657 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.656 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.656 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 1i36 | NAP | Conserved protein | / | 0.655 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.655 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.655 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.654 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.654 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.654 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.654 | |
| 4ros | APR | Malate dehydrogenase | / | 0.653 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.652 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.652 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.652 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.652 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.652 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.652 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.652 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.651 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.651 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.651 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.650 |