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 |
|---|---|---|---|
| 4lj6 | ACP | Chaperone protein ClpB |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4lj6 | ACP | Chaperone protein ClpB | / | 1.000 | |
| 4lj8 | ADP | Chaperone protein ClpB | / | 0.534 | |
| 4lj9 | ACP | Chaperone protein ClpB | / | 0.519 | |
| 1qvr | ANP | Chaperone protein ClpB | / | 0.511 | |
| 4fd2 | ADP | Chaperone protein ClpB | / | 0.507 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 4fcw | ADP | Chaperone protein ClpB | / | 0.485 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.477 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.472 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.471 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3dk1 | G05 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1c6y | MK1 | Protease | / | 0.458 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 1gqt | ACP | Ribokinase | / | 0.455 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.455 | |
| 3o9c | K20 | Pol polyprotein | / | 0.455 | |
| 3o9g | F53 | Gag-Pol polyprotein | / | 0.454 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.451 | |
| 3mxd | K53 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.450 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.450 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3ogq | AB1 | Pol polyprotein | / | 0.449 | |
| 3oy4 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 5dp2 | NAP | CurF | / | 0.449 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.449 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2bb9 | AKC | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2fdd | 385 | Pol protein | / | 0.448 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5c41 | ACP | Ribokinase | / | 0.448 | |
| 2qi3 | MZ5 | Gag-Pol polyprotein | / | 0.447 | |
| 4a4q | UX9 | Pol protein | / | 0.447 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1bwa | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 2qi6 | MZ8 | Gag-Pol polyprotein | / | 0.445 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.445 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3sa8 | K83 | Protease | / | 0.445 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.445 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2qd7 | 065 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2qi4 | MZ6 | Gag-Pol polyprotein | / | 0.444 | |
| 3bvb | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3kdd | JZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3ttp | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4q1y | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1b6k | PI5 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2q3k | MUW | Gag-Pol polyprotein | / | 0.443 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.443 | |
| 3gi5 | K62 | Gag-Pol polyprotein | / | 0.443 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3nbv | ANP | Ketohexokinase | / | 0.443 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.443 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.443 | |
| 1d4h | BEH | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1ec3 | MS3 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1hpx | KNI | Gag-Pol polyprotein | / | 0.442 | |
| 1hsg | MK1 | Gag-Pol polyprotein | / | 0.442 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3bxr | DRR | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3sm2 | 478 | Putative gag-pro-pol polyprotein | / | 0.442 | |
| 4q1w | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2q5k | AB1 | Protease | / | 0.441 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.441 | |
| 3liv | E16 | Protease | / | 0.441 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1sbg | IM1 | Gag-Pol polyprotein | / | 0.440 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2cdu | FAD | NADH oxidase | / | 0.440 | |
| 2i0d | MUT | Protease | / | 0.440 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3cyw | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.440 | |
| 3lzu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3o9a | K14 | Pol polyprotein | / | 0.440 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4njs | G08 | Protease | / | 0.440 |