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 |
|---|---|---|---|
| 3beo | UD1 | UDP-N-acetylglucosamine 2-epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3beo | UD1 | UDP-N-acetylglucosamine 2-epimerase | / | 1.000 | |
| 4fkz | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.603 | |
| 5dld | UD1 | UDP-N-Acetylglucosamine 2-epimerase | / | 0.488 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.479 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.470 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.469 | |
| 2b56 | UTP | RNA editing complex protein MP57 | / | 0.466 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.466 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.466 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.461 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.458 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.458 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.457 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.457 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.456 | |
| 4to5 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.456 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.456 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.454 | |
| 2x3j | ATP | AcsD | / | 0.454 | |
| 3f7b | AG5 | Carbonic anhydrase 4 | 4.2.1.1 | 0.454 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.454 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.453 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.452 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.451 | |
| 4lut | DCS | Alanine racemase | / | 0.451 | |
| 4zwe | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.451 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.450 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.449 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.448 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.448 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.447 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.446 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.446 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.446 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.445 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.444 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.444 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.444 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.443 | |
| 2quj | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.443 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.443 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.443 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.442 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.442 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.442 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 4rje | FNR | Lactate oxidase | / | 0.442 | |
| 1glf | ADP | Glycerol kinase | / | 0.441 | |
| 1p0y | SAH | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.441 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.441 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.441 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.440 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.440 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.440 |