sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1ib6 | NAD | Malate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ib6 | NAD | Malate dehydrogenase | / | 1.000 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.556 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.548 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.546 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.535 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.521 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.518 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.512 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.501 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.488 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.487 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.486 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.483 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.481 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.480 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.479 | |
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.478 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.474 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.474 | |
| 4ajj | 88R | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.474 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.471 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.469 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.468 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 4ajn | 88V | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.467 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.467 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.466 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.466 | |
| 4ros | APR | Malate dehydrogenase | / | 0.466 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.465 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.465 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.465 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.464 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.464 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.463 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.463 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.462 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.461 | |
| 3rn8 | RN8 | Glutamate receptor 2 | / | 0.461 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.459 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.458 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.458 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.457 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.457 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.456 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.456 | |
| 1d0m | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.455 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.455 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.454 | |
| 4al4 | W7E | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.454 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.453 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.452 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.452 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.451 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.451 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.451 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.451 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.450 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.450 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.450 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.449 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.449 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.449 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.449 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.449 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.448 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.448 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.448 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.447 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.447 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.446 | |
| 2rc4 | ACO | Histone acetyltransferase KAT6A | / | 0.446 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.446 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.446 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.445 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.445 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.445 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.445 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.445 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4l4x | NDP | AmphI | / | 0.445 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 1y7t | NDP | Malate dehydrogenase | / | 0.444 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.444 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.444 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.444 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.443 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.442 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.442 | |
| 2xfy | ACX | Beta-amylase | 3.2.1.2 | 0.442 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.442 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.442 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.441 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.441 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.441 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.441 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.440 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1u33 | LM2 | Pancreatic alpha-amylase | / | 0.440 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.440 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4e2d | FMN | Dehydrogenase | / | 0.440 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 | |
| 4jic | FMN | GTN Reductase | / | 0.440 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.440 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.440 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.440 |