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 |
|---|---|---|---|
| 3bxz | ADP | Protein translocase subunit SecA |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3bxz | ADP | Protein translocase subunit SecA | / | 0.952 | |
| 4o3m | ADP | Bloom syndrome protein | 3.6.4.12 | 0.755 | |
| 4ncl | GDP | Eukaryotic translation initiation factor 5B | / | 0.750 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.747 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.744 | |
| 4ys0 | ADP | Protein translocase subunit SecA | / | 0.743 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.737 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.737 | |
| 4luc | GDP | GTPase KRas | / | 0.730 | |
| 3cob | ADP | Kinesin heavy chain-like protein | / | 0.726 | |
| 2whx | ADP | Genome polyprotein | 3.4.21.91 | 0.724 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.721 | |
| 1bmf | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.720 | |
| 1bmf | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.720 | |
| 2zts | ADP | Uncharacterized protein | / | 0.720 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.720 | |
| 4l8g | GDP | GTPase KRas | / | 0.720 | |
| 5ftc | ADP | TPR domain protein | / | 0.720 | |
| 1z0f | GDP | Ras-related protein Rab-14 | / | 0.719 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.717 | |
| 1njf | ADP | DNA polymerase III subunit tau | 2.7.7.7 | 0.710 | |
| 4pjk | ADP | Myosin-2 heavy chain | / | 0.710 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.708 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.705 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.705 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.705 | |
| 3qbv | GDP | Cell division control protein 42 homolog | / | 0.704 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.703 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.703 | |
| 4m0l | GDP | Translation initiation factor 2 subunit gamma | / | 0.703 | |
| 4lv6 | GDP | GTPase KRas | / | 0.699 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.697 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.696 | |
| 4rz3 | ADP | Site-determining protein | / | 0.696 | |
| 2i1v | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.694 | |
| 2xae | ADP | Kinesin-like protein KIF11 | / | 0.694 | |
| 2v1x | ADP | ATP-dependent DNA helicase Q1 | 3.6.4.12 | 0.693 | |
| 3l9h | ADP | Kinesin-like protein KIF11 | / | 0.691 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.691 | |
| 1nly | AGS | Cag alpha | / | 0.690 | |
| 1oyy | AGS | ATP-dependent DNA helicase RecQ | 3.6.4.12 | 0.689 | |
| 4q03 | GDP | GTPase KRas | / | 0.689 | |
| 5aun | ADP | Iron-sulfur cluster carrier protein | / | 0.686 | |
| 1mmg | AGS | Myosin-2 heavy chain | / | 0.685 | |
| 4ldj | GDP | GTPase KRas | / | 0.685 | |
| 1n6m | ADP | Protein claret segregational | / | 0.684 | |
| 3k9l | GNP | GTPase HRas | / | 0.684 | |
| 2jj1 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.683 | |
| 2jj1 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.683 | |
| 4wa7 | GDP | GTPase KRas | / | 0.683 | |
| 2jj2 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.682 | |
| 2jj2 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.682 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.682 | |
| 4bzq | ADP | Bifunctional enzyme CysN/CysC | 2.7.1.25 | 0.682 | |
| 2uz3 | TTP | Thymidine kinase | / | 0.681 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.681 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.680 | |
| 4dsu | GDP | GTPase KRas | / | 0.680 | |
| 1jx2 | ADP | Myosin-2 heavy chain | / | 0.679 | |
| 1sdm | ADP | Kinesin heavy chain-like protein | / | 0.679 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.679 | |
| 4ma4 | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.679 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.678 | |
| 1rfq | ATP | Actin, alpha skeletal muscle | / | 0.677 | |
| 1xnj | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.677 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.677 | |
| 4qnr | ATP | Psp operon transcriptional activator | / | 0.677 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.676 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.676 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.676 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.676 | |
| 4a28 | ADP | Kinesin-like protein KIF11 | / | 0.676 | |
| 2ce7 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.675 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.675 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.674 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.674 | |
| 4epw | GDP | GTPase KRas | / | 0.674 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.672 | |
| 1xmv | ADP | Protein RecA | / | 0.672 | |
| 2fna | ADP | Uncharacterized protein | / | 0.672 | |
| 4dso | GSP | GTPase KRas | / | 0.672 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.671 | |
| 1wbb | ADP | DNA mismatch repair protein MutS | / | 0.671 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.670 | |
| 4ag5 | ADP | Type IV secretory pathway VirB4 components-like protein | / | 0.670 | |
| 4obe | GDP | GTPase KRas | / | 0.670 | |
| 3mle | ADP | ATP-dependent dethiobiotin synthetase BioD | 6.3.3.3 | 0.669 | |
| 4b7b | ADP | Kinesin-like protein KIF11 | / | 0.669 | |
| 4epx | GDP | GTPase KRas | / | 0.669 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.668 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.668 | |
| 4ql3 | GDP | GTPase KRas | / | 0.668 | |
| 2l0x | GDP | GTP-binding protein Rheb | / | 0.667 | |
| 4idn | GNP | Atlastin-1 | 3.6.5 | 0.667 | |
| 4pkg | ATP | Actin, alpha skeletal muscle | / | 0.667 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.666 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.666 | |
| 1dej | ATP | Major actin | / | 0.665 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.665 | |
| 2w2v | GTP | Ras-related C3 botulinum toxin substrate 2 | / | 0.665 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.665 | |
| 4z54 | GDP | Neuronal-specific septin-3 | / | 0.665 | |
| 1atn | ATP | Actin, alpha skeletal muscle | / | 0.664 | |
| 1w7k | ADP | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.664 | |
| 2ce2 | GDP | GTPase HRas | / | 0.664 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.664 | |
| 2vos | ADP | Folylpolyglutamate synthase | / | 0.664 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.664 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.663 | |
| 1h8h | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.663 | |
| 1h8h | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.663 | |
| 5ero | 210 | Fusicoccadiene synthase | 2.5.1.29 | 0.663 | |
| 1kxp | ATP | Actin, alpha skeletal muscle | / | 0.662 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.662 | |
| 2x2r | ADP | Kinesin-like protein KIF11 | / | 0.662 | |
| 4pk4 | ADP | Unconventional myosin-VI | / | 0.662 | |
| 1r0z | ATP | Cystic fibrosis transmembrane conductance regulator | / | 0.661 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.661 | |
| 2jiz | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.661 | |
| 3ffk | ATP | Actin, alpha skeletal muscle | / | 0.661 | |
| 3qi2 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.661 | |
| 4rzu | ADP | Probable thymidylate kinase | 2.7.4.9 | 0.661 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.660 | |
| 5c03 | AGS | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.660 | |
| 1mab | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.659 | |
| 1s22 | ATP | Actin, alpha skeletal muscle | / | 0.659 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.659 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.659 | |
| 4lrw | GDP | GTPase KRas | / | 0.659 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.658 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.658 | |
| 4cbx | ATP | Actin-2 | / | 0.658 | |
| 4jsy | GTP | Metallophosphoesterase | / | 0.658 | |
| 4l9s | GDP | GTPase HRas | / | 0.658 | |
| 4xjx | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.658 | |
| 1t31 | OHH | Chymase | 3.4.21.39 | 0.657 | |
| 3bb3 | GDP | Translocase of chloroplast 33, chloroplastic | 3.6.5 | 0.657 | |
| 4b1v | ATP | Actin, alpha skeletal muscle | / | 0.657 | |
| 4gp6 | ADP | Metallophosphoesterase | / | 0.657 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.657 | |
| 1w1w | AGS | Structural maintenance of chromosomes protein 1 | / | 0.656 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.656 | |
| 2r9v | ATP | ATP synthase subunit alpha | / | 0.656 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.656 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.656 | |
| 2zxu | DST | tRNA dimethylallyltransferase | 2.5.1.75 | 0.656 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.656 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.655 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.655 | |
| 1kqm | ANP | Myosin heavy chain, striated muscle | / | 0.655 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.655 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.655 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.655 | |
| 3kud | GDP | GTPase HRas | / | 0.655 | |
| 3q9l | ATP | Septum site-determining protein MinD | / | 0.655 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.655 | |
| 5cyo | GDP | Septin-9 | / | 0.655 | |
| 1rgi | ATP | Actin, alpha skeletal muscle | / | 0.654 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.654 | |
| 2fl2 | ADP | Kinesin-like protein KIF11 | / | 0.654 | |
| 3ldw | ZOL | Farnesyl pyrophosphate synthase, putative | / | 0.654 | |
| 2o8b | ADP | DNA mismatch repair protein Msh2 | / | 0.653 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.653 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.652 | |
| 2bc9 | GNP | Guanylate-binding protein 1 | / | 0.652 | |
| 4v02 | ATP | Site-determining protein | / | 0.652 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.651 | |
| 2cl6 | CAG | GTPase HRas | / | 0.651 | |
| 3ryw | K9H | Farnesyl pyrophosphate synthase, putative | / | 0.651 | |
| 4ram | PNM | Metallo-beta-lactamase type 2 | / | 0.651 | |
| 4ww0 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.651 | |
| 1k6m | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 | 2.7.1.105 | 0.650 | |
| 1q3h | ANP | Cystic fibrosis transmembrane conductance regulator | / | 0.650 | |
| 1um8 | ADP | ATP-dependent Clp protease ATP-binding subunit ClpX | / | 0.650 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.650 | |
| 3oee | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.650 | |
| 3oee | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.650 | |
| 4cdg | ADP | Bloom syndrome protein | 3.6.4.12 | 0.650 | |
| 4jlo | ADP | Adenylate kinase | / | 0.650 | |
| 4tq9 | GDP | GTPase KRas | / | 0.650 | |
| 5da9 | AGS | Uncharacterized protein | / | 0.650 |