sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4aff | ATP | Nitrogen regulatory protein P-II |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4aff | ATP | Nitrogen regulatory protein P-II | / | 1.000 | |
| 3ta2 | ATP | Nitrogen regulatory protein P-II (GlnB-3) | / | 0.560 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.482 | |
| 3i60 | E86 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.481 | |
| 5c03 | AGS | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.474 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.471 | |
| 2yfe | YFE | Peroxisome proliferator-activated receptor gamma | / | 0.467 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.466 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.465 | |
| 4mk0 | 29X | Beta-adrenergic receptor kinase 1 | 2.7.11.15 | 0.465 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.461 | |
| 3tjs | D0R | Cytochrome P450 3A4 | / | 0.460 | |
| 3vsp | EK8 | Peroxisome proliferator-activated receptor gamma | / | 0.459 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.458 | |
| 2ydx | STL | Methionine adenosyltransferase 2 subunit beta | / | 0.457 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.457 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 2hxl | 422 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.455 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.455 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.455 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.455 | |
| 4a4w | YFB | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.454 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.454 | |
| 1ffu | FAD | Carbon monoxide dehydrogenase medium chain | / | 0.453 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.453 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.451 | |
| 1qr0 | COA | 4'-phosphopantetheinyl transferase sfp | 2.7.8 | 0.451 | |
| 4h4q | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.451 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.450 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 3nie | ANP | Mitogen-activated protein kinase | / | 0.450 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.449 | |
| 1glf | ADP | Glycerol kinase | / | 0.448 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.448 | |
| 4h3q | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.447 | |
| 2ym6 | YM6 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.447 | |
| 4fd2 | ADP | Chaperone protein ClpB | / | 0.447 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.446 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.446 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3mhy | ATP | Nitrogen regulatory protein P-II 1 | / | 0.446 | |
| 3up5 | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4d03 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.445 | |
| 4i3z | ADP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.444 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.443 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.443 | |
| 3pxv | FMN | Nitroreductase | / | 0.443 | |
| 3tti | KBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.443 | |
| 4c4h | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.443 | |
| 4dee | ADP | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 4kwh | NAP | Reductase homolog | / | 0.443 | |
| 1agn | NAD | Alcohol dehydrogenase class 4 mu/sigma chain | 1.1.1.1 | 0.442 | |
| 1f3p | NAD | Ferredoxin reductase | / | 0.442 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.442 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.442 | |
| 2vgp | AD6 | Aurora kinase B-A | 2.7.11.1 | 0.442 | |
| 3ocp | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.442 | |
| 3pcf | FHB | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 3zon | IK1 | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.442 | |
| 4fg9 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.442 | |
| 1kvt | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2e20 | B4P | Propionate kinase | / | 0.441 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.441 | |
| 3my5 | RFZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.440 | |
| 4jaz | STL | Peroxisome proliferator-activated receptor gamma | / | 0.440 |