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 |
|---|---|---|---|
| 3ke1 | 829 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ke1 | 829 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 1.000 | |
| 3iew | CTP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.630 | |
| 4c8e | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.585 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.581 | |
| 1h47 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.576 | |
| 3k14 | 535 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.570 | |
| 1iv4 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.556 | |
| 3k2x | I5A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.529 | |
| 3f0g | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.505 | |
| 1gx1 | CDP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.499 | |
| 1h48 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.497 | |
| 1iv2 | CDP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.495 | |
| 3p0z | CTN | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.494 | |
| 2amt | 1AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.493 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.489 | |
| 4c8g | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.482 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.480 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.476 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.473 | |
| 2uzh | CDP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.471 | |
| 3elc | F01 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.471 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.468 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.468 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.467 | |
| 4gt3 | ATP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.467 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.466 | |
| 3rga | ILD | Epoxide hydrolase LasB | 5.5.1 | 0.464 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.463 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.458 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.457 | |
| 3t80 | CTN | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 4pd6 | URI | Nucleoside permease | / | 0.456 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.454 | |
| 2cdu | FAD | NADH oxidase | / | 0.454 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.454 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.454 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.454 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.454 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.454 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.453 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.452 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.452 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.450 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.449 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 1hk5 | T44 | Serum albumin | / | 0.448 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.448 | |
| 3dej | RXC | Caspase-3 | 3.4.22.56 | 0.447 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.447 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.445 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 3dei | RXB | Caspase-3 | 3.4.22.56 | 0.445 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.444 | |
| 1pr1 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.444 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.444 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.444 | |
| 4oh4 | ANP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.444 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.443 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.443 | |
| 2ojj | 82A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.442 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.442 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.442 | |
| 3zc5 | W9Z | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 1c0f | ATP | Major actin | / | 0.441 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 4a06 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4oac | ADP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.441 | |
| 3qft | NAP | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 3qtu | X44 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3sw7 | 19K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 |