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 |
|---|---|---|---|
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 1.148 | |
| 2dy9 | ADP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.808 | |
| 1lwx | AZD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.804 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.785 | |
| 4uof | DAT | Nucleoside diphosphate kinase | / | 0.784 | |
| 4fkx | CDP | Nucleoside diphosphate kinase | / | 0.772 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.765 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.757 | |
| 1zs6 | ADP | Nucleoside diphosphate kinase 3 | 2.7.4.6 | 0.752 | |
| 2dxe | GDP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.749 | |
| 2hvd | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.715 | |
| 3t3f | N5P | DNA polymerase I, thermostable | 2.7.7.7 | 0.690 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.685 | |
| 1p3j | AP5 | Adenylate kinase | / | 0.682 | |
| 3bbf | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.682 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.682 | |
| 4tlc | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.681 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.680 | |
| 3fbc | TYD | Nucleoside diphosphate kinase | 2.7.4.6 | 0.678 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.676 | |
| 1w1w | AGS | Structural maintenance of chromosomes protein 1 | / | 0.674 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.673 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.669 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.669 | |
| 4tlb | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.669 | |
| 4xcz | T3Q | Qdtf | / | 0.668 | |
| 5bsm | ATP | 4-coumarate--CoA ligase 2 | 6.2.1.12 | 0.667 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.665 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.665 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.665 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.665 | |
| 1dap | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.664 | |
| 1wc5 | APC | Adenylate cyclase | / | 0.663 | |
| 4lfv | YS4 | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.663 | |
| 4tl7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.663 | |
| 4xd1 | T3Q | Qdtf | / | 0.663 | |
| 2osb | AP5 | Adenylate kinase | / | 0.662 | |
| 1df7 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.661 | |
| 4qnr | ATP | Psp operon transcriptional activator | / | 0.661 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.660 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.659 | |
| 2gvd | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.659 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.658 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.658 | |
| 2e93 | B29 | Geranylgeranyl pyrophosphate synthase | / | 0.658 | |
| 2p0a | ANP | Synapsin-3 | / | 0.658 | |
| 1u0h | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.657 | |
| 3ez3 | ZOL | Farnesyl pyrophosphate synthase, putative | / | 0.657 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.657 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.656 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.656 | |
| 3tgp | GNP | GTPase HRas | / | 0.655 | |
| 3u9e | COA | Lmo1369 protein | / | 0.655 | |
| 4db1 | ANP | Myosin-7 | / | 0.655 | |
| 1f06 | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.654 | |
| 3g6x | DGT | DNA polymerase iota | 2.7.7.7 | 0.654 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.654 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.654 | |
| 5bnt | NAP | Aspartate-semialdehyde dehydrogenase | 1.2.1.11 | 0.654 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.653 | |
| 2r9v | ATP | ATP synthase subunit alpha | / | 0.653 | |
| 1bxr | ANP | Carbamoyl-phosphate synthase large chain | / | 0.652 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.652 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.651 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.651 | |
| 3lzx | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.651 | |
| 3rye | UNR | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.651 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.651 | |
| 1cq8 | PY6 | Aspartate aminotransferase | 2.6.1.1 | 0.650 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.650 | |
| 3vth | AP2 | Carbamoyltransferase | / | 0.650 | |
| 4kqs | RIS | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.650 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.650 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.650 |