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 |
|---|---|---|---|
| 1sxj | AGS | Replication factor C subunit 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1sxj | AGS | Replication factor C subunit 1 | / | 1.182 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.784 | |
| 1njf | AGS | DNA polymerase III subunit tau | 2.7.7.7 | 0.769 | |
| 1mmg | AGS | Myosin-2 heavy chain | / | 0.761 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.756 | |
| 1njf | ADP | DNA polymerase III subunit tau | 2.7.7.7 | 0.752 | |
| 1bmf | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.750 | |
| 1bmf | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.750 | |
| 1um8 | ADP | ATP-dependent Clp protease ATP-binding subunit ClpX | / | 0.747 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.746 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.745 | |
| 2cl6 | CAG | GTPase HRas | / | 0.742 | |
| 3hu3 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.737 | |
| 4ko8 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.737 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.735 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.734 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.733 | |
| 1w1w | AGS | Structural maintenance of chromosomes protein 1 | / | 0.731 | |
| 2jj1 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.730 | |
| 2jj1 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.730 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.730 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.730 | |
| 5bn3 | ADP | NEQ263 | / | 0.730 | |
| 1fmw | ATP | Myosin-2 heavy chain | / | 0.726 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.723 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.723 | |
| 3m0e | ATP | Transcriptional regulator (NtrC family) | / | 0.722 | |
| 1svl | ADP | Large T antigen | 3.6.4 | 0.718 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.716 | |
| 3dt4 | GTP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.715 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.714 | |
| 1a2b | GSP | Transforming protein RhoA | / | 0.713 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.713 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.712 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.711 | |
| 3b1x | GNP | Ferrous iron transport protein B | / | 0.710 | |
| 4xsg | GSP | Transforming protein RhoA | / | 0.710 | |
| 4ys0 | ADP | Protein translocase subunit SecA | / | 0.709 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.708 | |
| 2g1q | ADP | Kinesin-like protein KIF11 | / | 0.708 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.708 | |
| 4jsy | GTP | Metallophosphoesterase | / | 0.708 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.707 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.706 | |
| 2whx | ADP | Genome polyprotein | 3.4.21.91 | 0.705 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.704 | |
| 1wa5 | GTP | GTP-binding nuclear protein Ran | / | 0.704 | |
| 2qaj | AP5 | Adenylate kinase | / | 0.704 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.704 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.704 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.704 | |
| 5i4n | ATP | Tyrosine-protein kinase JAK2 | / | 0.704 | |
| 1yrs | ADP | Kinesin-like protein KIF11 | / | 0.703 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.701 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.701 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.700 | |
| 2x7e | ADP | Kinesin-like protein KIF11 | / | 0.700 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.700 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.699 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.699 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.698 | |
| 4ncl | GDP | Eukaryotic translation initiation factor 5B | / | 0.698 | |
| 4tle | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.698 | |
| 2c5l | GTP | GTPase HRas | / | 0.697 | |
| 2gcp | GSP | Rho-related GTP-binding protein RhoC | / | 0.697 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.697 | |
| 1ayl | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.696 | |
| 1svm | ATP | Large T antigen | 3.6.4 | 0.696 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.695 | |
| 1w5t | ADP | ORC1-type DNA replication protein 2 | / | 0.694 | |
| 2cls | GTP | Rho-related GTP-binding protein Rho6 | / | 0.694 | |
| 2xto | GDP | GTPase IMAP family member 2 | / | 0.694 | |
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.694 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.693 | |
| 2v7q | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.693 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.692 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.692 | |
| 2osb | AP5 | Adenylate kinase | / | 0.691 | |
| 4ki0 | ANP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.691 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.691 | |
| 3qe0 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.690 | |
| 4tl8 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.690 | |
| 3cf0 | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.689 | |
| 4dso | GSP | GTPase KRas | / | 0.689 | |
| 3bos | CDP | Regulatory inactivation of DnaA Hda protein | / | 0.688 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.688 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.688 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.688 | |
| 1aq2 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.687 | |
| 2fna | ADP | Uncharacterized protein | / | 0.687 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.687 | |
| 4wa7 | GDP | GTPase KRas | / | 0.686 | |
| 1h8h | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.685 | |
| 1h8h | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.685 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.685 | |
| 4tq9 | GDP | GTPase KRas | / | 0.685 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.684 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.684 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.684 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.684 | |
| 2bku | GTP | GTP-binding nuclear protein Ran | / | 0.684 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.684 | |
| 2r9v | ATP | ATP synthase subunit alpha | / | 0.684 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.684 | |
| 4dvg | GSP | Rho family GTPase | / | 0.684 | |
| 4xvu | ATP | ATPase GET3 | / | 0.684 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.683 | |
| 4lv6 | GDP | GTPase KRas | / | 0.683 | |
| 4ql3 | GDP | GTPase KRas | / | 0.683 | |
| 1ii6 | ADP | Kinesin-like protein KIF11 | / | 0.682 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.682 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.682 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.682 | |
| 4q03 | GDP | GTPase KRas | / | 0.682 | |
| 4qnr | ATP | Psp operon transcriptional activator | / | 0.682 | |
| 5ftc | ADP | TPR domain protein | / | 0.682 | |
| 2rgx | AP5 | Adenylate kinase | / | 0.681 | |
| 4epx | GDP | GTPase KRas | / | 0.681 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.681 | |
| 4hut | ATP | Cob(I)yrinic acid a,c-diamide adenosyltransferase | 2.5.1.17 | 0.681 | |
| 4o25 | GTP | GTP-binding protein Rheb | / | 0.681 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.680 | |
| 2oo7 | AP5 | Adenylate kinase | / | 0.680 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.680 | |
| 4nh0 | ATP | ESX secretion system protein EccC | / | 0.680 | |
| 1p3j | AP5 | Adenylate kinase | / | 0.679 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.679 | |
| 3x2v | ATP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.679 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.679 | |
| 1z0f | GDP | Ras-related protein Rab-14 | / | 0.678 | |
| 2fl2 | ADP | Kinesin-like protein KIF11 | / | 0.678 | |
| 3dkv | AP5 | Adenylate kinase | / | 0.678 | |
| 3x2w | ATP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.678 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.678 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.677 | |
| 4fvr | ATP | Tyrosine-protein kinase JAK2 | / | 0.677 | |
| 4l9s | GDP | GTPase HRas | / | 0.677 | |
| 3ews | ADP | ATP-dependent RNA helicase DDX19B | 3.6.4.13 | 0.676 | |
| 3law | GNP | Ras-related protein Rab-7a | / | 0.676 | |
| 1fp6 | ADP | Nitrogenase iron protein 1 | 1.18.6.1 | 0.675 | |
| 2e8w | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.675 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.675 | |
| 4pjk | ADP | Myosin-2 heavy chain | / | 0.675 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.674 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.674 | |
| 3bb3 | GDP | Translocase of chloroplast 33, chloroplastic | 3.6.5 | 0.674 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.674 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.674 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.673 | |
| 1e96 | GTP | Ras-related C3 botulinum toxin substrate 1 | / | 0.673 | |
| 2eu8 | AP5 | Adenylate kinase | / | 0.673 | |
| 2iut | AGS | DNA translocase FtsK | / | 0.673 | |
| 1e32 | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.672 | |
| 2fju | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.672 | |
| 3mhy | ATP | Nitrogen regulatory protein P-II 1 | / | 0.672 | |
| 4cei | ANP | ATP-dependent helicase/deoxyribonuclease subunit B | 3.1 | 0.672 | |
| 4g0n | GNP | GTPase HRas | / | 0.672 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.672 | |
| 4xjx | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.672 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.671 | |
| 1p3d | ANP | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.671 | |
| 2q2z | ADP | Kinesin-like protein KIF11 | / | 0.671 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.671 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.671 | |
| 3dt2 | GTP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.670 | |
| 3pfi | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.670 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.670 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.670 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.670 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.669 | |
| 4k81 | GTP | GTPase HRas | / | 0.669 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.668 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.668 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.667 | |
| 4epw | GDP | GTPase KRas | / | 0.667 | |
| 5jlj | GNP | GTP-binding nuclear protein Ran | / | 0.667 | |
| 1qz5 | ATP | Actin, alpha skeletal muscle | / | 0.666 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.666 | |
| 4jky | ADP | Adenylate kinase | / | 0.666 | |
| 4mkg | AP5 | Adenylate kinase | / | 0.666 | |
| 1vg8 | GNP | Ras-related protein Rab-7a | / | 0.665 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.665 | |
| 3k9l | GNP | GTPase HRas | / | 0.665 | |
| 3r9x | GNP | GTPase Era | / | 0.665 | |
| 3tgp | GNP | GTPase HRas | / | 0.665 | |
| 1ofh | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.664 | |
| 1pox | TPP | Pyruvate oxidase | 1.2.3.3 | 0.664 | |
| 4dlt | GNP | GTPase HRas | / | 0.664 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.664 | |
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 0.663 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.662 | |
| 1oyy | AGS | ATP-dependent DNA helicase RecQ | 3.6.4.12 | 0.662 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.662 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.662 | |
| 2v1x | ADP | ATP-dependent DNA helicase Q1 | 3.6.4.12 | 0.662 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.662 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.662 | |
| 4hdo | GNP | Ras-related protein Rap-1b | / | 0.662 | |
| 4mit | GTP | Rho-related protein racC | / | 0.662 | |
| 4w5j | AP5 | Adenylate kinase | / | 0.662 | |
| 3hqd | ANP | Kinesin-like protein KIF11 | / | 0.661 | |
| 4lja | ACP | Chaperone protein ClpB | / | 0.661 | |
| 4ymu | ATP | ABC-type polar amino acid transport system, ATPase component | / | 0.661 | |
| 1gp2 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.660 | |
| 1pow | TPP | Pyruvate oxidase | 1.2.3.3 | 0.660 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.660 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.660 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.660 | |
| 4mkf | AP5 | Adenylate kinase | / | 0.660 | |
| 3lbh | GNP | GTPase HRas | / | 0.659 | |
| 3lbi | GNP | GTPase HRas | / | 0.659 | |
| 5l3s | GNP | Signal recognition particle receptor FtsY | / | 0.659 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.658 | |
| 1r0z | ATP | Cystic fibrosis transmembrane conductance regulator | / | 0.658 | |
| 1wua | ATP | Actin, alpha skeletal muscle | / | 0.658 | |
| 1okk | GCP | Signal recognition particle protein | / | 0.657 | |
| 1okk | GCP | Signal recognition particle receptor FtsY | / | 0.657 | |
| 3vth | APC | Carbamoyltransferase | / | 0.657 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.657 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.656 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.656 | |
| 4dsu | GDP | GTPase KRas | / | 0.656 | |
| 4gzm | GSP | Ras-related C3 botulinum toxin substrate 1 | / | 0.656 | |
| 4wou | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.656 | |
| 2c96 | ATP | Psp operon transcriptional activator | / | 0.655 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.655 | |
| 2hf8 | GSP | Probable hydrogenase nickel incorporation protein HypB | / | 0.655 | |
| 3a4l | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.655 | |
| 4asu | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.655 | |
| 5dac | AGS | Uncharacterized protein | / | 0.655 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.654 | |
| 1im2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.654 | |
| 1ny5 | ADP | Transcriptional regulator (NtrC family) | / | 0.654 | |
| 2jj2 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.654 | |
| 2jj2 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.654 | |
| 2rgg | GNP | GTPase HRas | / | 0.654 | |
| 4lrw | GDP | GTPase KRas | / | 0.654 | |
| 1mab | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.653 | |
| 1ohh | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.653 | |
| 1ohh | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.653 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.653 | |
| 2ce2 | GDP | GTPase HRas | / | 0.653 | |
| 4r2l | ATP | Universal stress protein F | / | 0.653 | |
| 2pg2 | ADP | Kinesin-like protein KIF11 | / | 0.652 | |
| 1a5u | ATP | Pyruvate kinase PKM | 2.7.1.40 | 0.651 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.651 | |
| 2q36 | ATP | Actin, alpha skeletal muscle | / | 0.651 | |
| 3dl0 | AP5 | Adenylate kinase | / | 0.651 | |
| 4b7b | ADP | Kinesin-like protein KIF11 | / | 0.651 | |
| 4uxj | TTP | Thymidine kinase | / | 0.651 | |
| 1kxp | ATP | Actin, alpha skeletal muscle | / | 0.650 | |
| 3c41 | ANP | Amino acid ABC transporter | / | 0.650 | |
| 3oiu | GNP | GTPase HRas | / | 0.650 | |
| 4dls | GNP | GTPase HRas | / | 0.650 |