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 |
|---|---|---|---|
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.963 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.963 | |
| 2ck3 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.908 | |
| 2ck3 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.908 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.873 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.873 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.857 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.857 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.841 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.841 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.840 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.840 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.833 | |
| 2r9v | ATP | ATP synthase subunit alpha | / | 0.812 | |
| 3oee | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.808 | |
| 3oee | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.808 | |
| 1ohh | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.790 | |
| 1ohh | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.790 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.790 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.790 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.784 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.784 | |
| 2jj1 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.763 | |
| 3oeh | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.759 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.755 | |
| 4tlb | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.751 | |
| 4tlc | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.750 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.747 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.746 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.746 | |
| 4idn | GNP | Atlastin-1 | 3.6.5 | 0.739 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.735 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.728 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.725 | |
| 4v02 | ATP | Site-determining protein | / | 0.725 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.722 | |
| 4bec | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.722 | |
| 4tl8 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.721 | |
| 4jsy | GTP | Metallophosphoesterase | / | 0.719 | |
| 2fna | ADP | Uncharacterized protein | / | 0.718 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.718 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.717 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.717 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.716 | |
| 4asu | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.716 | |
| 4tle | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.716 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.714 | |
| 5bn3 | ADP | NEQ263 | / | 0.714 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.713 | |
| 4gp6 | ADP | Metallophosphoesterase | / | 0.713 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.711 | |
| 5ftc | ADP | TPR domain protein | / | 0.710 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.708 | |
| 1esn | ANP | Pantothenate kinase | 2.7.1.33 | 0.707 | |
| 4nh0 | ATP | ESX secretion system protein EccC | / | 0.707 | |
| 1bmf | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.706 | |
| 1bmf | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.706 | |
| 4tl9 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.704 | |
| 5i67 | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.704 | |
| 1khb | GCP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.703 | |
| 2x7e | ADP | Kinesin-like protein KIF11 | / | 0.703 | |
| 3b1x | GNP | Ferrous iron transport protein B | / | 0.703 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.702 | |
| 4xjx | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.702 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.701 | |
| 1ayl | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.700 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.700 | |
| 2jj1 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.700 | |
| 2jj1 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.700 | |
| 2jj2 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.700 | |
| 2jj2 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.700 | |
| 2zts | ADP | Uncharacterized protein | / | 0.700 | |
| 4lv6 | GDP | GTPase KRas | / | 0.700 | |
| 1xef | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.699 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.699 | |
| 4dso | GSP | GTPase KRas | / | 0.699 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.699 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.697 | |
| 4jlo | ADP | Adenylate kinase | / | 0.697 | |
| 4ncl | GDP | Eukaryotic translation initiation factor 5B | / | 0.697 | |
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.697 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.696 | |
| 1ny5 | ADP | Transcriptional regulator (NtrC family) | / | 0.696 | |
| 2bc9 | GNP | Guanylate-binding protein 1 | / | 0.696 | |
| 3ftq | GNP | Septin-2 | / | 0.696 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.696 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.695 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.695 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.694 | |
| 3fkq | ATP | NtrC-like two-domain protein | / | 0.694 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.693 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.693 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.693 | |
| 5aun | ADP | Iron-sulfur cluster carrier protein | / | 0.693 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.692 | |
| 3zfd | ANP | Chromosome-associated kinesin KIF4 | / | 0.692 | |
| 1t91 | GTP | Ras-related protein Rab-7a | / | 0.691 | |
| 2db3 | ANP | ATP-dependent RNA helicase vasa, isoform A | 3.6.4.13 | 0.691 | |
| 3myk | ANP | Myosin-2 heavy chain | / | 0.691 | |
| 1e1q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.690 | |
| 2cl6 | CAG | GTPase HRas | / | 0.690 | |
| 2jlr | ANP | Genome polyprotein | 3.4.21.91 | 0.690 | |
| 4r43 | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.690 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.690 | |
| 2c5l | GTP | GTPase HRas | / | 0.689 | |
| 2c96 | ATP | Psp operon transcriptional activator | / | 0.688 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.687 | |
| 4idp | GNP | Atlastin-1 | 3.6.5 | 0.687 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.687 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.686 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.686 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.686 | |
| 4db1 | ANP | Myosin-7 | / | 0.686 | |
| 4nyj | GNP | GTPase HRas | / | 0.686 | |
| 4tq9 | GDP | GTPase KRas | / | 0.686 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.685 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.685 | |
| 4tl7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.685 | |
| 1r0z | ATP | Cystic fibrosis transmembrane conductance regulator | / | 0.684 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.684 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.683 | |
| 3adc | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.683 | |
| 2g1q | ADP | Kinesin-like protein KIF11 | / | 0.682 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.682 | |
| 3fwy | ADP | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein | / | 0.682 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.682 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.682 | |
| 3th5 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.682 | |
| 4pjk | ADP | Myosin-2 heavy chain | / | 0.682 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.681 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.680 | |
| 1ow3 | GDP | Transforming protein RhoA | / | 0.680 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.680 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.680 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.680 | |
| 4xvu | ATP | ATPase GET3 | / | 0.680 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.680 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.679 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.679 | |
| 3cx8 | GSP | Guanine nucleotide-binding protein subunit alpha-13 | / | 0.679 | |
| 4xsg | GSP | Transforming protein RhoA | / | 0.679 | |
| 1w5t | ADP | ORC1-type DNA replication protein 2 | / | 0.678 | |
| 1wbb | ADP | DNA mismatch repair protein MutS | / | 0.678 | |
| 4jjz | ADP | Formate--tetrahydrofolate ligase | / | 0.678 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.677 | |
| 3tlx | ADP | Adenylate kinase 2 | / | 0.677 | |
| 3ddc | GNP | GTPase HRas | / | 0.676 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.676 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.675 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.675 | |
| 3i3s | GNP | GTPase HRas | / | 0.675 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.674 | |
| 2ov2 | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.674 | |
| 2v7q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.674 | |
| 3rs4 | GNP | GTPase HRas | / | 0.674 | |
| 3rs5 | GNP | GTPase HRas | / | 0.674 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.674 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.674 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.673 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.673 | |
| 2xae | ADP | Kinesin-like protein KIF11 | / | 0.673 | |
| 4ap0 | ADP | Kinesin-like protein KIF11 | / | 0.673 | |
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.673 | |
| 4dsu | GDP | GTPase KRas | / | 0.673 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.672 | |
| 1aq2 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.671 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.671 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.671 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.671 | |
| 2x2r | ADP | Kinesin-like protein KIF11 | / | 0.671 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.671 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.671 | |
| 4g0n | GNP | GTPase HRas | / | 0.671 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.670 | |
| 1rrg | GDP | ADP-ribosylation factor 1 | / | 0.670 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.670 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.670 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.670 | |
| 4xvq | GNP | GTPase HRas | / | 0.670 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.670 | |
| 4ylg | GDP | ADP-ribosylation factor 1, putative | / | 0.670 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.669 | |
| 3oiu | GNP | GTPase HRas | / | 0.669 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.669 | |
| 1h8h | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.668 | |
| 1h8h | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.668 | |
| 3lbh | GNP | GTPase HRas | / | 0.668 | |
| 3pfi | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.668 | |
| 1wa5 | GTP | GTP-binding nuclear protein Ran | / | 0.667 | |
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 0.667 | |
| 2rge | GNP | GTPase HRas | / | 0.666 | |
| 4jl6 | ADP | Adenylate kinase | / | 0.666 | |
| 4jld | ADP | Adenylate kinase | / | 0.666 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.665 | |
| 4lrw | GDP | GTPase KRas | / | 0.665 | |
| 2rgg | GNP | GTPase HRas | / | 0.664 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.664 | |
| 4ko8 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.664 | |
| 5ftf | ADP | TPR domain protein | / | 0.664 | |
| 1bif | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.663 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.663 | |
| 3a4l | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.663 | |
| 3thy | ADP | DNA mismatch repair protein Msh2 | / | 0.663 | |
| 4dlz | GNP | GTPase HRas | / | 0.663 | |
| 2w2v | GTP | Ras-related C3 botulinum toxin substrate 2 | / | 0.662 | |
| 4bzq | ADP | Bifunctional enzyme CysN/CysC | 2.7.1.25 | 0.662 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.662 | |
| 4lj9 | ACP | Chaperone protein ClpB | / | 0.662 | |
| 4lja | ACP | Chaperone protein ClpB | / | 0.662 | |
| 1z0f | GDP | Ras-related protein Rab-14 | / | 0.661 | |
| 4rkf | GNP | Ras-related protein Rab-3 | / | 0.661 | |
| 5la6 | GTP | Tubulin alpha-1B chain | / | 0.661 | |
| 3tgp | GNP | GTPase HRas | / | 0.660 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.660 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.660 | |
| 2j7p | GNP | Signal recognition particle protein | / | 0.659 | |
| 2j7p | GNP | Signal recognition particle receptor FtsY | / | 0.659 | |
| 2o8b | ADP | DNA mismatch repair protein Msh2 | / | 0.659 | |
| 4l9w | GNP | GTPase HRas | / | 0.659 | |
| 1njf | ADP | DNA polymerase III subunit tau | 2.7.7.7 | 0.658 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.658 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.658 | |
| 3k1j | ADP | ATP-dependent protease Lon | / | 0.658 | |
| 5l3s | GNP | Signal recognition particle receptor FtsY | / | 0.658 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.657 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.657 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.657 | |
| 3mle | ADP | ATP-dependent dethiobiotin synthetase BioD | 6.3.3.3 | 0.657 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.657 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.657 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.656 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.656 | |
| 4m0l | GDP | Translation initiation factor 2 subunit gamma | / | 0.656 | |
| 4r9u | ANP | Vitamin B12 import ATP-binding protein BtuD | / | 0.656 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.655 | |
| 1sdm | ADP | Kinesin heavy chain-like protein | / | 0.654 | |
| 2pg2 | ADP | Kinesin-like protein KIF11 | / | 0.654 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.654 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.654 | |
| 1mma | ADP | Myosin-2 heavy chain | / | 0.653 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.653 | |
| 4d81 | ADP | AAA ATPase, central domain protein | / | 0.653 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.653 | |
| 4x8l | AP5 | Adenylate kinase | / | 0.653 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.652 | |
| 4dzz | ADP | Plasmid partitioning protein ParF | / | 0.652 | |
| 4iok | ADP | Formate--tetrahydrofolate ligase | / | 0.652 | |
| 4ww0 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.652 | |
| 2q2y | ADP | Kinesin-like protein KIF11 | / | 0.651 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.651 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.651 | |
| 2rgb | GNP | GTPase HRas | / | 0.650 | |
| 2zfi | ADP | Kinesin-like protein KIF1A | / | 0.650 | |
| 5dac | AGS | Uncharacterized protein | / | 0.650 |