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 |
|---|---|---|---|
| 4tv9 | GTP | Tubulin alpha-1B chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 1.393 | |
| 4tuy | GTP | Tubulin alpha-1B chain | / | 1.365 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 1.348 | |
| 4o4l | GTP | Tubulin alpha-1B chain | / | 1.342 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 1.337 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 1.323 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 1.318 | |
| 5la6 | GTP | Tubulin alpha-1B chain | / | 1.313 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 1.286 | |
| 4o4i | GTP | Tubulin alpha-1B chain | / | 1.252 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 1.242 | |
| 3ryh | GTP | Tubulin alpha chain | / | 1.234 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 1.188 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.917 | |
| 4ffb | GTP | Tubulin alpha-1 chain | / | 0.908 | |
| 3zid | GDP | Tubulin-like protein CetZ | / | 0.904 | |
| 5la6 | GDP | Tubulin beta-2B chain | / | 0.814 | |
| 1z5v | GSP | Tubulin gamma-1 chain | / | 0.800 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.768 | |
| 2bto | GTP | Tubulin | / | 0.765 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.757 | |
| 2xul | ATP | Nitrogen regulatory protein P-II | / | 0.708 | |
| 2xka | GSP | Cell division protein FtsZ | / | 0.703 | |
| 1bif | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.698 | |
| 2r6r | GDP | Cell division protein FtsZ | / | 0.695 | |
| 3m0e | ATP | Transcriptional regulator (NtrC family) | / | 0.694 | |
| 4xjx | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.692 | |
| 1z5w | GTP | Tubulin gamma-1 chain | / | 0.688 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.687 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.686 | |
| 3mhy | ATP | Nitrogen regulatory protein P-II 1 | / | 0.686 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.684 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.684 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.684 | |
| 4nu0 | AP5 | Adenylate kinase | / | 0.681 | |
| 1ayl | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.677 | |
| 4ej7 | ATP | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.677 | |
| 1aq2 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.675 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.675 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.674 | |
| 3hiy | UTP | Uncharacterized protein | / | 0.674 | |
| 2oan | ATP | Actin, cytoplasmic 1 | / | 0.672 | |
| 4pki | ATP | Actin, alpha skeletal muscle | / | 0.668 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.668 | |
| 3wt0 | ATP | Cell division protein FtsA | / | 0.666 | |
| 4dwb | 0M7 | Farnesyl pyrophosphate synthase | / | 0.666 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.666 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.665 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.665 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.665 | |
| 4ga3 | 4GA | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.665 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.665 | |
| 3dkv | AP5 | Adenylate kinase | / | 0.664 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.663 | |
| 4dso | GSP | GTPase KRas | / | 0.663 | |
| 1mmg | AGS | Myosin-2 heavy chain | / | 0.662 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.662 | |
| 3ftq | GNP | Septin-2 | / | 0.662 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.662 | |
| 1fmw | ATP | Myosin-2 heavy chain | / | 0.661 | |
| 2a41 | ATP | Actin, alpha skeletal muscle | / | 0.661 | |
| 2q0l | NAP | Thioredoxin reductase | 1.8.1.9 | 0.661 | |
| 4tlb | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.661 | |
| 4tlc | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.661 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.660 | |
| 4mkf | AP5 | Adenylate kinase | / | 0.660 | |
| 3rs4 | GNP | GTPase HRas | / | 0.659 | |
| 3rs7 | GNP | GTPase HRas | / | 0.659 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.659 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.658 | |
| 4tl7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.658 | |
| 1ih8 | APC | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.657 | |
| 4ccq | NAP | Thioredoxin reductase | / | 0.657 | |
| 5i4n | ATP | Tyrosine-protein kinase JAK2 | / | 0.657 | |
| 2cvx | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.656 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.656 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.655 | |
| 3a5o | ATP | Major actin | / | 0.655 | |
| 4qfy | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.655 | |
| 2pz8 | APC | NH(3)-dependent NAD(+) synthetase | / | 0.654 | |
| 3s87 | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.654 | |
| 3myk | ANP | Myosin-2 heavy chain | / | 0.653 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.651 | |
| 3v2u | ATP | Protein GAL3 | / | 0.651 | |
| 4w5j | AP5 | Adenylate kinase | / | 0.651 | |
| 1c0f | ATP | Major actin | / | 0.650 | |
| 1n2e | APC | Pantothenate synthetase | 6.3.2.1 | 0.650 |