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 |
|---|---|---|---|
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 1.036 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.939 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.903 | |
| 4a62 | ANP | Plasmid segregation protein ParM | / | 0.801 | |
| 4ehu | ANP | 2-hydroxyisocaproyl-CoA dehydratase activator | / | 0.798 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.761 | |
| 1eqy | ATP | Actin, alpha skeletal muscle | / | 0.750 | |
| 1kxp | ATP | Actin, alpha skeletal muscle | / | 0.745 | |
| 4b1v | ATP | Actin, alpha skeletal muscle | / | 0.742 | |
| 1dej | ATP | Major actin | / | 0.732 | |
| 1c0f | ATP | Major actin | / | 0.731 | |
| 1rgi | ATP | Actin, alpha skeletal muscle | / | 0.729 | |
| 1t44 | ATP | Actin, alpha skeletal muscle | / | 0.729 | |
| 1qz5 | ATP | Actin, alpha skeletal muscle | / | 0.727 | |
| 1s22 | ATP | Actin, alpha skeletal muscle | / | 0.727 | |
| 4k41 | ATP | Actin, alpha skeletal muscle | / | 0.727 | |
| 1rfq | ATP | Actin, alpha skeletal muscle | / | 0.723 | |
| 1atn | ATP | Actin, alpha skeletal muscle | / | 0.719 | |
| 5ce3 | ATP | Actin | / | 0.718 | |
| 3eks | ATP | Actin-5C | / | 0.716 | |
| 3wt0 | ATP | Cell division protein FtsA | / | 0.713 | |
| 1yxq | ATP | Actin, alpha skeletal muscle | / | 0.712 | |
| 2q36 | ATP | Actin, alpha skeletal muscle | / | 0.711 | |
| 4pki | ATP | Actin, alpha skeletal muscle | / | 0.711 | |
| 4pkg | ATP | Actin, alpha skeletal muscle | / | 0.701 | |
| 3a5m | ATP | Major actin | / | 0.700 | |
| 4jhd | ANP | Actin-5C | / | 0.695 | |
| 3a5o | ATP | Major actin | / | 0.693 | |
| 3m1f | ATP | Actin, alpha skeletal muscle | / | 0.693 | |
| 3w3d | ATP | Actin, gamma-enteric smooth muscle | / | 0.693 | |
| 2a41 | ATP | Actin, alpha skeletal muscle | / | 0.692 | |
| 4cbx | ATP | Actin-2 | / | 0.692 | |
| 1mdu | ATP | Actin, alpha skeletal muscle | / | 0.689 | |
| 3daw | ATP | Actin, alpha skeletal muscle | / | 0.688 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.686 | |
| 2cvu | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.684 | |
| 3m6g | ATP | Actin, alpha skeletal muscle | / | 0.684 | |
| 3chw | ATP | Major actin | / | 0.682 | |
| 2q97 | ATP | Actin, alpha skeletal muscle | / | 0.681 | |
| 3ffk | ATP | Actin, alpha skeletal muscle | / | 0.681 | |
| 1x09 | IPE | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.679 | |
| 3tu5 | ATP | Actin, alpha skeletal muscle | / | 0.679 | |
| 4mkf | AP5 | Adenylate kinase | / | 0.679 | |
| 3rye | UNR | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.678 | |
| 3tb9 | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.678 | |
| 1zw5 | ZOL | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.677 | |
| 4nu0 | AP5 | Adenylate kinase | / | 0.677 | |
| 4w5j | AP5 | Adenylate kinase | / | 0.677 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.675 | |
| 3dvl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.675 | |
| 4lfv | YS4 | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.675 | |
| 2v51 | ATP | Actin, alpha skeletal muscle | / | 0.674 | |
| 3eku | ATP | Actin-5C | / | 0.674 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.670 | |
| 4kh0 | ATP | Aspartate carbamoyltransferase regulatory chain {ECO:0000256|HAMAP-Rule:MF_00002} | / | 0.670 | |
| 2wzb | ADP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.669 | |
| 3rqq | BA3 | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 0.669 | |
| 4nke | RIS | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.669 | |
| 4h5c | YS4 | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.668 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.668 | |
| 2cvv | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.667 | |
| 1xs4 | DCP | dCTP deaminase | / | 0.666 | |
| 4dwb | 0M7 | Farnesyl pyrophosphate synthase | / | 0.666 | |
| 4b9q | ATP | Chaperone protein DnaK | / | 0.664 | |
| 4q23 | RIS | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.663 | |
| 3m0e | ATP | Transcriptional regulator (NtrC family) | / | 0.660 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.660 | |
| 4dem | YS4 | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.659 | |
| 3ar4 | ATP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.658 | |
| 4h5e | YS4 | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.658 | |
| 1n2g | APC | Pantothenate synthetase | 6.3.2.1 | 0.657 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.657 | |
| 3ez3 | ZOL | Farnesyl pyrophosphate synthase, putative | / | 0.657 | |
| 4dxj | 0M9 | Farnesyl pyrophosphate synthase | / | 0.657 | |
| 3vth | APC | Carbamoyltransferase | / | 0.655 | |
| 4tnp | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.655 | |
| 2e2q | ADP | ATP-dependent hexokinase | / | 0.654 | |
| 3krf | DST | Geranyl diphosphate synthase large subunit | / | 0.653 | |
| 3zoz | ADP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.653 | |
| 1rqj | RIS | Farnesyl diphosphate synthase | 2.5.1.10 | 0.652 | |
| 1ijj | ATP | Actin, alpha skeletal muscle | / | 0.650 | |
| 5bsm | ATP | 4-coumarate--CoA ligase 2 | 6.2.1.12 | 0.650 |