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 |
|---|---|---|---|
| 3qop | CMP | cAMP-activated global transcriptional regulator CRP |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3qop | CMP | cAMP-activated global transcriptional regulator CRP | / | 1.000 | |
| 3kcc | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.684 | |
| 4r8h | SP1 | cAMP-activated global transcriptional regulator CRP | / | 0.660 | |
| 3rou | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.646 | |
| 4i01 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.626 | |
| 4ft8 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.623 | |
| 1zrc | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.621 | |
| 1zrd | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.619 | |
| 2gzw | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.618 | |
| 4i09 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.612 | |
| 3rpq | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.611 | |
| 4hzf | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.577 | |
| 3ryp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.575 | |
| 4i0a | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.575 | |
| 1i5z | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.553 | |
| 2oz6 | CMP | Cyclic AMP receptor-like protein | / | 0.486 | |
| 1vce | SAH | Diphthine synthase | / | 0.483 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.483 | |
| 2egs | SAH | Diphthine synthase | / | 0.480 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.479 | |
| 2ejj | SAH | Diphthine synthase | / | 0.478 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.477 | |
| 2ehl | SAH | Diphthine synthase | / | 0.476 | |
| 4hj6 | FMN | LOV protein | / | 0.476 | |
| 2dsh | SAH | Diphthine synthase | / | 0.475 | |
| 2dxv | SAH | Diphthine synthase | / | 0.475 | |
| 2egb | SAH | Diphthine synthase | / | 0.475 | |
| 2owk | SAH | Diphthine synthase | / | 0.474 | |
| 2p5f | SAH | Diphthine synthase | / | 0.474 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.474 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.472 | |
| 2emu | SAH | Diphthine synthase | / | 0.472 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.472 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.471 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.471 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.470 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.468 | |
| 2p6d | SAH | Diphthine synthase | / | 0.467 | |
| 2dxw | SAH | Diphthine synthase | / | 0.466 | |
| 2eka | SAH | Diphthine synthase | / | 0.466 | |
| 2hut | SAH | Diphthine synthase | / | 0.466 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.466 | |
| 2owu | SAH | Diphthine synthase | / | 0.465 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.464 | |
| 2p5c | SAH | Diphthine synthase | / | 0.463 | |
| 2e16 | SAH | Diphthine synthase | / | 0.462 | |
| 1vp6 | CMP | Cyclic nucleotide-gated potassium channel mll3241 | / | 0.461 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.461 | |
| 2huq | SAH | Diphthine synthase | / | 0.461 | |
| 2owf | SAH | Diphthine synthase | / | 0.461 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.460 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 3flw | FLW | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2eld | SAH | Diphthine synthase | / | 0.458 | |
| 2pck | SAH | Diphthine synthase | / | 0.458 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.458 | |
| 4kwh | NAP | Reductase homolog | / | 0.458 | |
| 4nak | PBQ | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic | 2.7.7.60 | 0.458 | |
| 2k0g | CMP | Cyclic nucleotide-gated potassium channel mll3241 | / | 0.457 | |
| 2qfo | A51 | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2e8r | SAH | Diphthine synthase | / | 0.456 | |
| 2p6i | SAH | Diphthine synthase | / | 0.456 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.456 | |
| 2pcm | SAH | Diphthine synthase | / | 0.456 | |
| 4dxd | 9PC | Cell division protein FtsZ | / | 0.455 | |
| 4fkr | 45K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2dek | SAH | Diphthine synthase | / | 0.453 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.453 | |
| 2z6r | SAH | Diphthine synthase | / | 0.453 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.453 | |
| 1gqt | ACP | Ribokinase | / | 0.452 | |
| 2e15 | SAH | Diphthine synthase | / | 0.452 | |
| 2ele | SAH | Diphthine synthase | / | 0.452 | |
| 2en5 | SAH | Diphthine synthase | / | 0.452 | |
| 2p9d | SAH | Diphthine synthase | / | 0.452 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.452 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2e8q | SAH | Diphthine synthase | / | 0.451 | |
| 2ejk | SAH | Diphthine synthase | / | 0.451 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.450 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.450 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.450 | |
| 2eni | SAH | Diphthine synthase | / | 0.450 | |
| 2p6k | SAH | Diphthine synthase | / | 0.450 | |
| 2pch | SAH | Diphthine synthase | / | 0.450 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3b89 | 5GP | 16S rRNA methylase | / | 0.450 | |
| 1ruo | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.449 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.449 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.449 | |
| 2emr | SAH | Diphthine synthase | / | 0.449 | |
| 2owg | SAH | Diphthine synthase | / | 0.449 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.449 | |
| 3v8t | 477 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.449 | |
| 3vob | 9PC | Cell division protein FtsZ | / | 0.449 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.448 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2el0 | SAH | Diphthine synthase | / | 0.447 | |
| 2huv | SAH | Diphthine synthase | / | 0.447 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.447 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.447 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.447 | |
| 4jbo | WPH | Aurora kinase A | 2.7.11.1 | 0.447 | |
| 2pcg | SAH | Diphthine synthase | / | 0.446 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.446 | |
| 4fkj | 11K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 2eeq | SAH | Diphthine synthase | / | 0.445 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.445 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.445 | |
| 3kc3 | MK2 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.444 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2e07 | SAH | Diphthine synthase | / | 0.443 | |
| 2q70 | DC8 | Estrogen receptor | / | 0.443 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.443 | |
| 4fg9 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.443 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.442 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.442 | |
| 2e8h | SAH | Diphthine synthase | / | 0.442 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.442 | |
| 4hbn | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.442 | |
| 4r8q | ADP | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 2.7.11.1 | 0.442 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.442 | |
| 1ke6 | LS2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.441 | |
| 2dxx | SAH | Diphthine synthase | / | 0.441 | |
| 3fln | 3FN | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.441 | |
| 3kfm | KAI | Glutamate receptor 4 | / | 0.441 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.441 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4f65 | 0S9 | Fibroblast growth factor receptor 1 | / | 0.441 | |
| 4qpm | ADP | Mitotic checkpoint serine/threonine-protein kinase BUB1 | 2.7.11.1 | 0.441 | |
| 4z07 | PCG | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.441 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.440 | |
| 1scu | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.440 | |
| 2dsg | SAH | Diphthine synthase | / | 0.440 | |
| 2ejz | SAH | Diphthine synthase | / | 0.440 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.440 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 |