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 |
|---|---|---|---|
| 2axn | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2axn | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | / | 1.137 | |
| 4ma4 | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 1.036 | |
| 2i1v | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.994 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.988 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.982 | |
| 1k6m | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 | 2.7.1.105 | 0.901 | |
| 1bif | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.870 | |
| 1xnj | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.790 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.779 | |
| 2x2r | ADP | Kinesin-like protein KIF11 | / | 0.779 | |
| 3nbx | ADP | ATPase RavA | 3.6.3 | 0.778 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.778 | |
| 2zrj | AGS | Protein RecA | / | 0.771 | |
| 3cob | ADP | Kinesin heavy chain-like protein | / | 0.770 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.766 | |
| 4b7b | ADP | Kinesin-like protein KIF11 | / | 0.766 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.766 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.766 | |
| 2fna | ADP | Uncharacterized protein | / | 0.759 | |
| 1sdm | ADP | Kinesin heavy chain-like protein | / | 0.758 | |
| 4a1z | ADP | Kinesin-like protein KIF11 | / | 0.758 | |
| 4z54 | GDP | Neuronal-specific septin-3 | / | 0.758 | |
| 3mle | ADP | ATP-dependent dethiobiotin synthetase BioD | 6.3.3.3 | 0.755 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.754 | |
| 2zro | ADP | Protein RecA | / | 0.750 | |
| 2zfi | ADP | Kinesin-like protein KIF1A | / | 0.749 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.749 | |
| 4gp6 | ADP | Metallophosphoesterase | / | 0.749 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.748 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.747 | |
| 2vf7 | ADP | UvrABC system protein A | / | 0.747 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.746 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.744 | |
| 4luc | GDP | GTPase KRas | / | 0.744 | |
| 1mmg | AGS | Myosin-2 heavy chain | / | 0.743 | |
| 2x7e | ADP | Kinesin-like protein KIF11 | / | 0.743 | |
| 4ag5 | ADP | Type IV secretory pathway VirB4 components-like protein | / | 0.743 | |
| 4asu | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.742 | |
| 1b7t | ADP | Myosin heavy chain, striated muscle | / | 0.740 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.740 | |
| 1wbb | ADP | DNA mismatch repair protein MutS | / | 0.739 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.738 | |
| 2fah | GDP | Phosphoenolpyruvate carboxykinase [GTP], mitochondrial | 4.1.1.32 | 0.738 | |
| 2pg2 | ADP | Kinesin-like protein KIF11 | / | 0.737 | |
| 3fwy | ADP | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein | / | 0.737 | |
| 4hi0 | GDP | Urease accessory protein UreG | / | 0.737 | |
| 3l9h | ADP | Kinesin-like protein KIF11 | / | 0.733 | |
| 3qbv | GDP | Cell division control protein 42 homolog | / | 0.732 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.732 | |
| 4obe | GDP | GTPase KRas | / | 0.731 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.731 | |
| 2ax4 | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 | 2.7.1.25 | 0.730 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.730 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.729 | |
| 2zts | ADP | Uncharacterized protein | / | 0.728 | |
| 4l8g | GDP | GTPase KRas | / | 0.728 | |
| 4tq9 | GDP | GTPase KRas | / | 0.728 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.727 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.727 | |
| 3ieu | GDP | GTPase Era | / | 0.725 | |
| 4epw | GDP | GTPase KRas | / | 0.725 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.724 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.724 | |
| 4ihq | ADP | Conserved Archaeal protein | / | 0.724 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.723 | |
| 4ap0 | ADP | Kinesin-like protein KIF11 | / | 0.723 | |
| 4epx | GDP | GTPase KRas | / | 0.723 | |
| 4lv6 | GDP | GTPase KRas | / | 0.723 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.722 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.722 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.720 | |
| 2fl2 | ADP | Kinesin-like protein KIF11 | / | 0.719 | |
| 1g6o | ADP | Cag alpha | / | 0.718 | |
| 4zca | ADP | Kinesin-like protein KIF11 | / | 0.718 | |
| 2ce7 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.717 | |
| 4m0l | GDP | Translation initiation factor 2 subunit gamma | / | 0.717 | |
| 3ftq | GNP | Septin-2 | / | 0.716 | |
| 3m0e | ATP | Transcriptional regulator (NtrC family) | / | 0.716 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.714 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.714 | |
| 4wa7 | GDP | GTPase KRas | / | 0.714 | |
| 3cf0 | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.713 | |
| 4q02 | GDP | GTPase KRas | / | 0.712 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.711 | |
| 2bif | ANP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.710 | |
| 5cyo | GDP | Septin-9 | / | 0.710 | |
| 2bc9 | GNP | Guanylate-binding protein 1 | / | 0.709 | |
| 1ii6 | ADP | Kinesin-like protein KIF11 | / | 0.708 | |
| 4r43 | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.708 | |
| 5ftc | ADP | TPR domain protein | / | 0.708 | |
| 2jj2 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.707 | |
| 2jj2 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.707 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.706 | |
| 4lrw | GDP | GTPase KRas | / | 0.706 | |
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 0.705 | |
| 4iok | ADP | Formate--tetrahydrofolate ligase | / | 0.705 | |
| 2ncd | ADP | Protein claret segregational | / | 0.704 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.704 | |
| 4ncl | GDP | Eukaryotic translation initiation factor 5B | / | 0.704 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.703 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.703 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.703 | |
| 1ht2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.702 | |
| 4k81 | GTP | GTPase HRas | / | 0.701 | |
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.701 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.700 | |
| 3tgp | GNP | GTPase HRas | / | 0.700 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.699 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.699 | |
| 2zpa | ADP | tRNA(Met) cytidine acetyltransferase TmcA | / | 0.699 | |
| 4bzq | ADP | Bifunctional enzyme CysN/CysC | 2.7.1.25 | 0.698 | |
| 4idp | GNP | Atlastin-1 | 3.6.5 | 0.698 | |
| 4jjz | ADP | Formate--tetrahydrofolate ligase | / | 0.698 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.698 | |
| 1e32 | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.697 | |
| 2dr3 | ADP | UPF0273 protein PH0284 | / | 0.697 | |
| 5i67 | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.697 | |
| 1mma | ADP | Myosin-2 heavy chain | / | 0.696 | |
| 4a28 | ADP | Kinesin-like protein KIF11 | / | 0.696 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.696 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.694 | |
| 3thy | ADP | DNA mismatch repair protein Msh2 | / | 0.694 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.694 | |
| 4o3m | ADP | Bloom syndrome protein | 3.6.4.12 | 0.694 | |
| 1q3h | ANP | Cystic fibrosis transmembrane conductance regulator | / | 0.693 | |
| 3c41 | ANP | Amino acid ABC transporter | / | 0.693 | |
| 1jx2 | ADP | Myosin-2 heavy chain | / | 0.691 | |
| 2g1q | ADP | Kinesin-like protein KIF11 | / | 0.691 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.691 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.691 | |
| 5bn3 | ADP | NEQ263 | / | 0.691 | |
| 4ldj | GDP | GTPase KRas | / | 0.690 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.690 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.689 | |
| 1f5n | GNP | Guanylate-binding protein 1 | / | 0.689 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.689 | |
| 4ql3 | GDP | GTPase KRas | / | 0.689 | |
| 4dlt | GNP | GTPase HRas | / | 0.687 | |
| 4nh0 | ATP | ESX secretion system protein EccC | / | 0.687 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.686 | |
| 3cx8 | GSP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.686 | |
| 3k8y | GNP | GTPase HRas | / | 0.686 | |
| 4lpk | GDP | GTPase KRas | / | 0.686 | |
| 4wou | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.686 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.685 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.685 | |
| 1lfd | GNP | GTPase HRas | / | 0.685 | |
| 1svw | GTP | Probable GTP-binding protein EngB | / | 0.685 | |
| 2xae | ADP | Kinesin-like protein KIF11 | / | 0.685 | |
| 3bb3 | GDP | Translocase of chloroplast 33, chloroplastic | 3.6.5 | 0.685 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.685 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.685 | |
| 4l9s | GDP | GTPase HRas | / | 0.684 | |
| 1ayl | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.683 | |
| 3k1j | ADP | ATP-dependent protease Lon | / | 0.683 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.682 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.682 | |
| 2q2z | ADP | Kinesin-like protein KIF11 | / | 0.682 | |
| 4a51 | ADP | Kinesin-like protein KIF11 | / | 0.682 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.679 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.679 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.679 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.678 | |
| 2o8b | ADP | DNA mismatch repair protein Msh2 | / | 0.678 | |
| 3oee | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.676 | |
| 3oee | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.676 | |
| 1g41 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.675 | |
| 2c9c | ATP | Psp operon transcriptional activator | / | 0.675 | |
| 2rgg | GNP | GTPase HRas | / | 0.675 | |
| 1n6m | ADP | Protein claret segregational | / | 0.674 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.674 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.674 | |
| 2xto | GDP | GTPase IMAP family member 2 | / | 0.674 | |
| 1rrg | GDP | ADP-ribosylation factor 1 | / | 0.673 | |
| 4q03 | GDP | GTPase KRas | / | 0.673 | |
| 2ck3 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.672 | |
| 2ck3 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.672 | |
| 5ftf | ADP | TPR domain protein | / | 0.672 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.671 | |
| 2ce2 | GDP | GTPase HRas | / | 0.671 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.671 | |
| 4ww0 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.671 | |
| 2rgb | GNP | GTPase HRas | / | 0.670 | |
| 3ddc | GNP | GTPase HRas | / | 0.670 | |
| 3q9l | ATP | Septum site-determining protein MinD | / | 0.670 | |
| 4dlv | GNP | GTPase HRas | / | 0.670 | |
| 1um8 | ADP | ATP-dependent Clp protease ATP-binding subunit ClpX | / | 0.669 | |
| 1xd9 | ADP | Nitrogenase iron protein 1 | 1.18.6.1 | 0.669 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.669 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.668 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.668 | |
| 1h8h | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.668 | |
| 1h8h | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.668 | |
| 1zcb | GDP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.668 | |
| 3l1c | ADP | Protein claret segregational | / | 0.668 | |
| 1im2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.667 | |
| 1yra | GDP | GPN-loop GTPase PAB0955 | / | 0.667 | |
| 1evj | NAD | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.666 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.666 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.666 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.665 | |
| 4kod | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.665 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.664 | |
| 4idn | GNP | Atlastin-1 | 3.6.5 | 0.664 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.663 | |
| 4i1v | ADP | Dephospho-CoA kinase | / | 0.661 | |
| 4pjj | ADP | Unconventional myosin-VI | / | 0.661 | |
| 1xmv | ADP | Protein RecA | / | 0.660 | |
| 2gbl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.660 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.659 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.658 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.658 | |
| 2rge | GNP | GTPase HRas | / | 0.658 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.658 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.657 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.656 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.656 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.656 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.656 | |
| 3kud | GDP | GTPase HRas | / | 0.656 | |
| 3dvl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.655 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.654 | |
| 5c3c | ADP | CbbQ/NirQ/NorQ domain protein | / | 0.654 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.653 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.653 | |
| 1s3s | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.653 | |
| 3r9i | ADP | Septum site-determining protein MinD | / | 0.653 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.653 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.652 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.652 | |
| 4dfk | 0L5 | DNA polymerase I, thermostable | 2.7.7.7 | 0.652 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.652 | |
| 4mkf | AP5 | Adenylate kinase | / | 0.652 | |
| 4gzl | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.651 | |
| 1xp8 | AGS | Protein RecA | / | 0.650 | |
| 4jlo | ADP | Adenylate kinase | / | 0.650 | |
| 4pjk | ADP | Myosin-2 heavy chain | / | 0.650 |