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 |
|---|---|---|---|
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 1.000 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.706 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.555 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.542 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.536 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.515 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.514 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.511 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.506 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.498 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.496 | |
| 4ros | APR | Malate dehydrogenase | / | 0.494 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.489 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.484 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.481 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.480 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.478 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.476 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.475 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.475 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.474 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.471 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.471 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.470 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.469 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.467 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.467 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.466 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.466 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.465 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.463 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.463 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.463 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.462 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.460 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.460 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.459 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.458 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.458 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.457 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.457 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.457 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.457 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.457 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.457 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.456 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.456 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.456 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.455 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.453 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.453 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.453 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.452 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.452 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.451 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.450 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.450 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.450 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.450 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.450 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.449 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.449 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.449 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.449 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.449 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.448 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.448 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.448 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.448 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.448 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.448 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.448 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.448 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.447 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.447 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.447 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.446 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.446 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.446 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.446 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.446 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.446 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.446 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.445 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.445 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.445 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.445 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.444 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.444 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.444 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.442 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.442 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 4qec | NAP | ElxO | / | 0.442 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.441 | |
| 3a3g | DLZ | Lumazine protein | / | 0.441 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.440 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.440 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.440 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.440 | |
| 3vvp | BNU | Uncharacterized protein | / | 0.440 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 5a3b | APR | SIR2 family protein | / | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.440 |