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 Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2c98 | ADP | Psp operon transcriptional activator |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2c98 | ADP | Psp operon transcriptional activator | / | 0.909 | |
| 4qos | ADP | Psp operon transcriptional activator | / | 0.755 | |
| 3pfi | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.721 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.711 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.711 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.705 | |
| 5aun | ADP | Iron-sulfur cluster carrier protein | / | 0.705 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.702 | |
| 4jlo | ADP | Adenylate kinase | / | 0.702 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.700 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.700 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.699 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.695 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.694 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.694 | |
| 3ea0 | ATP | ATPase, ParA family | / | 0.694 | |
| 2fna | ADP | Uncharacterized protein | / | 0.692 | |
| 3cx6 | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.692 | |
| 3qbv | GDP | Cell division control protein 42 homolog | / | 0.692 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.689 | |
| 4gp6 | ADP | Metallophosphoesterase | / | 0.689 | |
| 2v7q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.688 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.688 | |
| 4dso | GSP | GTPase KRas | / | 0.687 | |
| 4lj7 | MNT | Chaperone protein ClpB | / | 0.687 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.684 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.684 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.682 | |
| 4jl6 | ADP | Adenylate kinase | / | 0.681 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.680 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.680 | |
| 1xnj | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.678 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.678 | |
| 4epw | GDP | GTPase KRas | / | 0.678 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.677 | |
| 4lv6 | GDP | GTPase KRas | / | 0.677 | |
| 3m0e | ATP | Transcriptional regulator (NtrC family) | / | 0.676 | |
| 3ref | GDP | Rho family GTPase | / | 0.676 | |
| 4q02 | GDP | GTPase KRas | / | 0.676 | |
| 4wa7 | GDP | GTPase KRas | / | 0.676 | |
| 4tq9 | GDP | GTPase KRas | / | 0.675 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.674 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.673 | |
| 1z0f | GDP | Ras-related protein Rab-14 | / | 0.672 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.671 | |
| 2x2r | ADP | Kinesin-like protein KIF11 | / | 0.671 | |
| 3fkq | ATP | NtrC-like two-domain protein | / | 0.671 | |
| 3fwy | ADP | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein | / | 0.671 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.670 | |
| 4dsu | GDP | GTPase KRas | / | 0.669 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.668 | |
| 2cl6 | CAG | GTPase HRas | / | 0.668 | |
| 4a28 | ADP | Kinesin-like protein KIF11 | / | 0.668 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.668 | |
| 5bn3 | ADP | NEQ263 | / | 0.668 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.667 | |
| 4q03 | GDP | GTPase KRas | / | 0.667 | |
| 4l9s | GDP | GTPase HRas | / | 0.666 | |
| 1w5t | ADP | ORC1-type DNA replication protein 2 | / | 0.665 | |
| 4jld | ADP | Adenylate kinase | / | 0.665 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.665 | |
| 4epx | GDP | GTPase KRas | / | 0.663 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.662 | |
| 4lpk | GDP | GTPase KRas | / | 0.662 | |
| 4obe | GDP | GTPase KRas | / | 0.662 | |
| 4xsg | GSP | Transforming protein RhoA | / | 0.661 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.660 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.659 | |
| 1yra | GDP | GPN-loop GTPase PAB0955 | / | 0.656 | |
| 2zts | ADP | Uncharacterized protein | / | 0.655 | |
| 3kjg | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.655 | |
| 4v02 | ATP | Site-determining protein | / | 0.655 | |
| 1ny5 | ADP | Transcriptional regulator (NtrC family) | / | 0.654 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.654 | |
| 1i4l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.653 | |
| 1nbm | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.653 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.653 | |
| 4xvq | GNP | GTPase HRas | / | 0.653 | |
| 4m0l | GDP | Translation initiation factor 2 subunit gamma | / | 0.652 | |
| 4pk4 | ADP | Unconventional myosin-VI | / | 0.652 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.651 | |
| 4itr | GDP | Cell division control protein 42 homolog | / | 0.651 | |
| 1k6m | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 | 2.7.1.105 | 0.650 | |
| 3k1j | ADP | ATP-dependent protease Lon | / | 0.650 |