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 Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 1.000 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.577 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.548 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.543 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.534 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.533 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.533 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.531 | |
| 1gv0 | NAD | Malate dehydrogenase | / | 0.528 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.525 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.525 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.521 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.519 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.517 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.516 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.515 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.513 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.508 | |
| 4ros | APR | Malate dehydrogenase | / | 0.508 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.506 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.504 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.504 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.502 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.502 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.500 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.500 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.499 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.499 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.494 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.493 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.492 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.491 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.491 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.490 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.490 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.488 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.488 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.487 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.486 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.486 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.486 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.486 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.481 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.480 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.480 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.479 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.479 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.477 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.477 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.477 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.472 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.472 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.471 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.471 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.471 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.471 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.470 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.470 | |
| 4ajn | 88V | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.470 | |
| 5dp2 | NAP | CurF | / | 0.470 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.468 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.468 | |
| 3m6i | NAD | L-arabinitol 4-dehydrogenase | 1.1.1.12 | 0.467 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.466 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.465 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.464 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.463 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.462 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.462 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.462 | |
| 1hf3 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.459 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.459 | |
| 5cdt | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.459 | |
| 1b8u | NAD | Malate dehydrogenase | / | 0.458 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.458 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.458 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.456 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.456 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.456 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.456 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.455 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.455 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.455 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.455 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.454 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.454 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.454 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.453 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.453 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.453 | |
| 5a3b | APR | SIR2 family protein | / | 0.453 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.452 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.452 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.452 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.451 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.451 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.451 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.451 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.451 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.450 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.450 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.449 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.448 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.448 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.447 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.447 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.447 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.447 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.446 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1wzi | NDP | Malate dehydrogenase | / | 0.446 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.446 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.446 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.446 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.446 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.445 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.444 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.444 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.444 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.444 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.444 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 1gqt | ACP | Ribokinase | / | 0.443 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 1efk | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.442 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.442 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.442 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.442 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.442 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.442 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.442 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.441 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.441 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.441 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.441 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.441 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.440 | |
| 3hwr | NDP | 2-dehydropantoate 2-reductase | / | 0.440 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.440 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.440 |