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 |
|---|---|---|---|
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 1.171 | |
| 4bec | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.912 | |
| 4xjx | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.871 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.776 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.768 | |
| 5l3s | GNP | Signal recognition particle receptor FtsY | / | 0.768 | |
| 4idn | GNP | Atlastin-1 | 3.6.5 | 0.759 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.757 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.756 | |
| 2bc9 | GNP | Guanylate-binding protein 1 | / | 0.743 | |
| 3adc | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.742 | |
| 4beb | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.742 | |
| 1esn | ANP | Pantothenate kinase | 2.7.1.33 | 0.741 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.740 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.739 | |
| 4g0n | GNP | GTPase HRas | / | 0.736 | |
| 3k9l | GNP | GTPase HRas | / | 0.735 | |
| 4xvu | ATP | ATPase GET3 | / | 0.731 | |
| 4v02 | ATP | Site-determining protein | / | 0.730 | |
| 1z2c | GNP | Rho-related GTP-binding protein RhoC | / | 0.728 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.728 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.726 | |
| 2jlr | ANP | Genome polyprotein | 3.4.21.91 | 0.724 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.722 | |
| 3tnf | GNP | Ras-related protein Rab-8A | / | 0.722 | |
| 1kmq | GNP | Transforming protein RhoA | / | 0.721 | |
| 1okk | GCP | Signal recognition particle protein | / | 0.721 | |
| 1okk | GCP | Signal recognition particle receptor FtsY | / | 0.721 | |
| 2db3 | ANP | ATP-dependent RNA helicase vasa, isoform A | 3.6.4.13 | 0.720 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.719 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.718 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.717 | |
| 3v4f | GNP | GTPase HRas | / | 0.717 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.715 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.715 | |
| 2hf8 | GSP | Probable hydrogenase nickel incorporation protein HypB | / | 0.715 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.714 | |
| 2qme | GCP | Ras-related C3 botulinum toxin substrate 3 | / | 0.713 | |
| 3a4l | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.713 | |
| 3rab | GNP | Ras-related protein Rab-3A | / | 0.713 | |
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.713 | |
| 3fkq | ATP | NtrC-like two-domain protein | / | 0.712 | |
| 5b2z | GNP | GTPase HRas | / | 0.711 | |
| 1m2o | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.710 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.709 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.707 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.707 | |
| 1fp6 | ADP | Nitrogenase iron protein 1 | 1.18.6.1 | 0.706 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.706 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.706 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.704 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.703 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.703 | |
| 3rs4 | GNP | GTPase HRas | / | 0.703 | |
| 4cei | ANP | ATP-dependent helicase/deoxyribonuclease subunit B | 3.1 | 0.703 | |
| 4q02 | GDP | GTPase KRas | / | 0.701 | |
| 2c96 | ATP | Psp operon transcriptional activator | / | 0.699 | |
| 4dsn | GCP | GTPase KRas | / | 0.699 | |
| 3dt2 | GTP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.698 | |
| 3dt4 | GTP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.698 | |
| 4kvg | GTP | Ras-related protein Rap-1A | / | 0.698 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.697 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.697 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.697 | |
| 1zc3 | GNP | Ras-related protein Ral-A | / | 0.696 | |
| 4w5j | AP5 | Adenylate kinase | / | 0.696 | |
| 2j7p | GNP | Signal recognition particle protein | / | 0.695 | |
| 2j7p | GNP | Signal recognition particle receptor FtsY | / | 0.695 | |
| 3q9l | ATP | Septum site-determining protein MinD | / | 0.695 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.695 | |
| 4c2u | ANP | DNA helicase | / | 0.694 | |
| 1z0f | GDP | Ras-related protein Rab-14 | / | 0.693 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.692 | |
| 1s1c | GNP | Transforming protein RhoA | / | 0.690 | |
| 2cl6 | CAG | GTPase HRas | / | 0.690 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.690 | |
| 3rs7 | GNP | GTPase HRas | / | 0.690 | |
| 4lrw | GDP | GTPase KRas | / | 0.689 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.688 | |
| 4qnr | ATP | Psp operon transcriptional activator | / | 0.687 | |
| 5l3r | GCP | Cell division protein FtsY homolog, chloroplastic | / | 0.687 | |
| 4qos | ADP | Psp operon transcriptional activator | / | 0.686 | |
| 2rgg | GNP | GTPase HRas | / | 0.685 | |
| 4idp | GNP | Atlastin-1 | 3.6.5 | 0.684 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.683 | |
| 3lbh | GNP | GTPase HRas | / | 0.683 | |
| 3oee | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.683 | |
| 3oee | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.683 | |
| 4dls | GNP | GTPase HRas | / | 0.683 | |
| 3c41 | ANP | Amino acid ABC transporter | / | 0.682 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.682 | |
| 4nh0 | ATP | ESX secretion system protein EccC | / | 0.682 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.682 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.680 | |
| 3k3b | ADP | Kinesin-like protein KIF11 | / | 0.680 | |
| 4tq9 | GDP | GTPase KRas | / | 0.679 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.678 | |
| 3ddc | GNP | GTPase HRas | / | 0.678 | |
| 3eg5 | GNP | Cell division control protein 42 homolog | / | 0.678 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.678 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.677 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.677 | |
| 3kud | GDP | GTPase HRas | / | 0.676 | |
| 3myk | ANP | Myosin-2 heavy chain | / | 0.676 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.675 | |
| 2ck3 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.675 | |
| 2ck3 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.675 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.675 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.675 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.674 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.674 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.673 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.673 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.673 | |
| 2r9v | ATP | ATP synthase subunit alpha | / | 0.673 | |
| 3hu1 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.673 | |
| 4jsy | GTP | Metallophosphoesterase | / | 0.673 | |
| 2ce2 | GDP | GTPase HRas | / | 0.672 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.672 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.672 | |
| 4epx | GDP | GTPase KRas | / | 0.672 | |
| 4k81 | GTP | GTPase HRas | / | 0.672 | |
| 4xvq | GNP | GTPase HRas | / | 0.672 | |
| 3tgp | GNP | GTPase HRas | / | 0.670 | |
| 4dvg | GSP | Rho family GTPase | / | 0.670 | |
| 4ohv | ANP | Protein clpf-1 | / | 0.670 | |
| 1rj9 | GCP | Signal recognition particle receptor FtsY | / | 0.669 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.669 | |
| 2ffq | GSP | Ras-related protein Rab-6B | / | 0.668 | |
| 4c30 | ANP | DNA helicase | / | 0.668 | |
| 4mit | GTP | Rho-related protein racC | / | 0.668 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.667 | |
| 4dlw | GNP | GTPase HRas | / | 0.666 | |
| 1lfd | GNP | GTPase HRas | / | 0.665 | |
| 5k5z | ANP | Uncharacterized protein | / | 0.665 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.664 | |
| 4q03 | GDP | GTPase KRas | / | 0.664 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.662 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.662 | |
| 3hqd | ANP | Kinesin-like protein KIF11 | / | 0.661 | |
| 4xsg | GSP | Transforming protein RhoA | / | 0.661 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.660 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.660 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.660 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.660 | |
| 3moh | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.660 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.660 | |
| 1nsf | ATP | Vesicle-fusing ATPase | 3.6.4.6 | 0.659 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.659 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.659 | |
| 5bn3 | ADP | NEQ263 | / | 0.659 | |
| 1cul | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.658 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.658 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.658 | |
| 1i4l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.658 | |
| 3oiu | GNP | GTPase HRas | / | 0.658 | |
| 1w5t | ADP | ORC1-type DNA replication protein 2 | / | 0.657 | |
| 3kjg | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.657 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.657 | |
| 4ql3 | GDP | GTPase KRas | / | 0.657 | |
| 4wou | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.657 | |
| 4dso | GSP | GTPase KRas | / | 0.656 | |
| 1e0j | ANP | DNA primase/helicase | 2.7.7 | 0.655 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.654 | |
| 4js0 | GNP | Cell division control protein 42 homolog | / | 0.654 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.653 | |
| 3k8y | GNP | GTPase HRas | / | 0.653 | |
| 3x1w | GDP | Ras-related protein Rap-1b | / | 0.653 | |
| 1ny5 | ADP | Transcriptional regulator (NtrC family) | / | 0.652 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.652 | |
| 2bme | GNP | Ras-related protein Rab-4A | / | 0.652 | |
| 1e79 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.651 | |
| 1e79 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.651 | |
| 1gp2 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.651 | |
| 1zio | AP5 | Adenylate kinase | / | 0.651 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.651 | |
| 3q5d | GDP | Atlastin-1 | 3.6.5 | 0.651 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.650 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.650 |