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 |
|---|---|---|---|
| 5c3z | ACP | Ribokinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5c3z | ACP | Ribokinase | / | 1.000 | |
| 5c3y | AN2 | Ribokinase | / | 0.658 | |
| 5c41 | ACP | Ribokinase | / | 0.607 | |
| 1gqt | ACP | Ribokinase | / | 0.554 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.548 | |
| 3lki | ATP | Fructokinase | / | 0.541 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.534 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.528 | |
| 1lik | ADN | Adenosine kinase | 2.7.1.20 | 0.523 | |
| 3nbv | ANP | Ketohexokinase | / | 0.513 | |
| 3umo | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.500 | |
| 3q92 | XNB | Ketohexokinase | / | 0.497 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.493 | |
| 2f02 | ATP | Tagatose-6-phosphate kinase | / | 0.491 | |
| 2hw1 | ANP | Ketohexokinase | / | 0.487 | |
| 3otx | AP5 | Adenosine kinase, putative | / | 0.483 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.479 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.474 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.474 | |
| 3qai | XNN | Ketohexokinase | / | 0.473 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.472 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.472 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.468 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.467 | |
| 3in1 | ADP | Uncharacterized sugar kinase YdjH | 2.7.1 | 0.467 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.465 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.464 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.463 | |
| 2dcn | ADP | 2-keto-3-deoxy-gluconate kinase | / | 0.461 | |
| 1ppj | ANY | Cytochrome b | / | 0.460 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.460 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.459 | |
| 5c40 | ACP | Ribokinase | / | 0.458 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.457 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2i5b | ADP | Pyridoxine kinase | / | 0.456 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.455 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.455 | |
| 2ab8 | ACP | Adenosine kinase | 2.7.1.20 | 0.454 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.452 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.452 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.452 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.451 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3rus | ADP | Chaperonin | / | 0.451 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.450 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 3ruq | ADP | Chaperonin | / | 0.450 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.450 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.450 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.450 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.450 | |
| 5cvf | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.450 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 3nbw | TR4 | Ketohexokinase | / | 0.448 | |
| 3nc9 | TR3 | Ketohexokinase | / | 0.448 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.448 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.447 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.447 | |
| 1xkd | NAP | Isocitrate dehydrogenase [NADP] | / | 0.446 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.446 | |
| 1rkd | ADP | Ribokinase | / | 0.445 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.445 | |
| 4fv5 | EK9 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.445 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 3qa2 | XNA | Ketohexokinase | / | 0.444 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.444 | |
| 4mkh | AP5 | Adenylate kinase | / | 0.444 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.444 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.443 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.443 | |
| 4lj9 | ACP | Chaperone protein ClpB | / | 0.443 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.442 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.441 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 4awi | AQ2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.440 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.440 |