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 |
|---|---|---|---|
| 3zl8 | ADP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3zl8 | ADP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 1.136 | |
| 3qcz | ANP | Dihydrofolate synthase/folylpolyglutamate synthase | / | 0.840 | |
| 1p3d | ANP | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.827 | |
| 1gqy | ACP | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.798 | |
| 2vos | ADP | Folylpolyglutamate synthase | / | 0.785 | |
| 1w7k | ADP | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.770 | |
| 1e4v | AP5 | Adenylate kinase | / | 0.755 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.752 | |
| 1z0d | GDP | Ras-related protein Rab-5C | / | 0.750 | |
| 2vor | ACP | Folylpolyglutamate synthase | / | 0.750 | |
| 3pyz | ANP | Dihydrofolate synthase/folylpolyglutamate synthase | / | 0.750 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.747 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.746 | |
| 4jl5 | ADP | Adenylate kinase | / | 0.745 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.739 | |
| 2rgx | AP5 | Adenylate kinase | / | 0.738 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.738 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.736 | |
| 4asu | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.735 | |
| 4jsy | GTP | Metallophosphoesterase | / | 0.730 | |
| 2fgj | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.727 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.727 | |
| 4r9u | ANP | Vitamin B12 import ATP-binding protein BtuD | / | 0.727 | |
| 4gp6 | ADP | Metallophosphoesterase | / | 0.725 | |
| 4i1v | ADP | Dephospho-CoA kinase | / | 0.718 | |
| 1rrg | GDP | ADP-ribosylation factor 1 | / | 0.717 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.716 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.716 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.715 | |
| 4y0v | GDP | ADP-ribosylation factor 1, putative | / | 0.715 | |
| 4ylg | GDP | ADP-ribosylation factor 1, putative | / | 0.715 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.713 | |
| 1xef | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.712 | |
| 4jky | ADP | Adenylate kinase | / | 0.711 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.710 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.708 | |
| 4dsn | GCP | GTPase KRas | / | 0.708 | |
| 4ihq | ADP | Conserved Archaeal protein | / | 0.708 | |
| 4qbg | AP5 | Adenylate kinase | / | 0.708 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.707 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.704 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.703 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.702 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.702 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.702 | |
| 4jl6 | ADP | Adenylate kinase | / | 0.702 | |
| 1ake | AP5 | Adenylate kinase | / | 0.701 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.701 | |
| 4jjz | ADP | Formate--tetrahydrofolate ligase | / | 0.701 | |
| 4cvl | ACP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.700 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.700 | |
| 1got | GDP | Guanine nucleotide-binding protein G(t) subunit alpha-1 | / | 0.699 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.699 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.699 | |
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 0.699 | |
| 2ck3 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.699 | |
| 2ck3 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.699 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.699 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.699 | |
| 1e4y | AP5 | Adenylate kinase | / | 0.698 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.698 | |
| 3a4l | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.698 | |
| 3hpr | AP5 | Adenylate kinase | / | 0.698 | |
| 4iok | ADP | Formate--tetrahydrofolate ligase | / | 0.697 | |
| 1g6o | ADP | Cag alpha | / | 0.696 | |
| 1yra | GDP | GPN-loop GTPase PAB0955 | / | 0.696 | |
| 2ic5 | GNP | Ras-related C3 botulinum toxin substrate 3 | / | 0.696 | |
| 3q9l | ATP | Septum site-determining protein MinD | / | 0.696 | |
| 4tl9 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.696 | |
| 4xsg | GSP | Transforming protein RhoA | / | 0.696 | |
| 3r9x | GNP | GTPase Era | / | 0.695 | |
| 1cxz | GSP | Transforming protein RhoA | / | 0.694 | |
| 2eck | ADP | Adenylate kinase | / | 0.694 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.694 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.693 | |
| 1q3h | ANP | Cystic fibrosis transmembrane conductance regulator | / | 0.693 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.693 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.693 | |
| 4jlo | ADP | Adenylate kinase | / | 0.693 | |
| 3kuc | GDP | Ras-related protein Rap-1A | / | 0.692 | |
| 4ike | ADP | Adenylate kinase | / | 0.692 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.691 | |
| 4bub | ADP | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase | / | 0.691 | |
| 4x8o | AP5 | Adenylate kinase | / | 0.691 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.690 | |
| 3tdk | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.688 | |
| 4qos | ADP | Psp operon transcriptional activator | / | 0.688 | |
| 5i67 | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.688 | |
| 3ftq | GNP | Septin-2 | / | 0.687 | |
| 2zfi | ADP | Kinesin-like protein KIF1A | / | 0.686 | |
| 4ldj | GDP | GTPase KRas | / | 0.686 | |
| 4cei | ANP | ATP-dependent helicase/deoxyribonuclease subunit B | 3.1 | 0.685 | |
| 5ftf | ADP | TPR domain protein | / | 0.684 | |
| 2gks | ADP | Probable bifunctional SAT/APS kinase | 2.7.1.25 | 0.683 | |
| 2jj1 | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.683 | |
| 2jj1 | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.683 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.683 | |
| 4yqf | GDP | Septin-9 | / | 0.683 | |
| 1wbb | ADP | DNA mismatch repair protein MutS | / | 0.682 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.682 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.682 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.682 | |
| 3c41 | ANP | Amino acid ABC transporter | / | 0.682 | |
| 4b7b | ADP | Kinesin-like protein KIF11 | / | 0.682 | |
| 1ht2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.681 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.681 | |
| 2pg2 | ADP | Kinesin-like protein KIF11 | / | 0.681 | |
| 2x7e | ADP | Kinesin-like protein KIF11 | / | 0.681 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.681 | |
| 5cyo | GDP | Septin-9 | / | 0.679 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.677 | |
| 4v02 | ATP | Site-determining protein | / | 0.677 | |
| 1fp6 | ADP | Nitrogenase iron protein 1 | 1.18.6.1 | 0.676 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.676 | |
| 4m0l | GDP | Translation initiation factor 2 subunit gamma | / | 0.675 | |
| 2fna | ADP | Uncharacterized protein | / | 0.674 | |
| 2zrj | AGS | Protein RecA | / | 0.674 | |
| 4xoi | GTP | Transforming protein RhoA | / | 0.674 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.673 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.672 | |
| 1gwn | GTP | Rho-related GTP-binding protein RhoE | / | 0.672 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.672 | |
| 2fl2 | ADP | Kinesin-like protein KIF11 | / | 0.672 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.671 | |
| 2ce2 | GDP | GTPase HRas | / | 0.671 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.671 | |
| 1bof | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.670 | |
| 2gm1 | ADP | Kinesin-like protein KIF11 | / | 0.670 | |
| 2q2z | ADP | Kinesin-like protein KIF11 | / | 0.670 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.670 | |
| 4xvq | GNP | GTPase HRas | / | 0.670 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.669 | |
| 2vf7 | ADP | UvrABC system protein A | / | 0.669 | |
| 4xvu | ATP | ATPase GET3 | / | 0.669 | |
| 2xae | ADP | Kinesin-like protein KIF11 | / | 0.668 | |
| 4idp | GNP | Atlastin-1 | 3.6.5 | 0.667 | |
| 1mab | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.665 | |
| 3hu3 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.665 | |
| 3r9i | ADP | Septum site-determining protein MinD | / | 0.665 | |
| 4hse | ADP | Chaperone protein ClpB | / | 0.665 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.665 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.665 | |
| 4tle | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.665 | |
| 1xms | ANP | Protein RecA | / | 0.664 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.664 | |
| 2osb | AP5 | Adenylate kinase | / | 0.664 | |
| 2pc9 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.664 | |
| 3sbd | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.664 | |
| 4dvg | GSP | Rho family GTPase | / | 0.664 | |
| 5ftc | ADP | TPR domain protein | / | 0.664 | |
| 3tlx | ADP | Adenylate kinase 2 | / | 0.663 | |
| 4ki0 | ANP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.663 | |
| 4luc | GDP | GTPase KRas | / | 0.663 | |
| 4oi2 | ADP | Protein clpf-1 | / | 0.663 | |
| 4tlb | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.663 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.663 | |
| 3lbh | GNP | GTPase HRas | / | 0.662 | |
| 4r43 | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.662 | |
| 1s3s | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.661 | |
| 3pfi | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.660 | |
| 4rz3 | ADP | Site-determining protein | / | 0.660 | |
| 2bc9 | GNP | Guanylate-binding protein 1 | / | 0.659 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.659 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.659 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.659 | |
| 4nh0 | ATP | ESX secretion system protein EccC | / | 0.659 | |
| 5fsx | ADP | Uncharacterized protein | / | 0.659 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.658 | |
| 3ddc | GNP | GTPase HRas | / | 0.658 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.657 | |
| 1ofh | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.657 | |
| 2l0x | GDP | GTP-binding protein Rheb | / | 0.657 | |
| 3b1x | GNP | Ferrous iron transport protein B | / | 0.657 | |
| 1bmf | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.656 | |
| 1bmf | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.656 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.656 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.656 | |
| 2c9o | ADP | RuvB-like 1 | 3.6.4.12 | 0.656 | |
| 4idn | GNP | Atlastin-1 | 3.6.5 | 0.656 | |
| 4wou | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.656 | |
| 1aq2 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.655 | |
| 1hsk | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.655 | |
| 3kud | GDP | GTPase HRas | / | 0.655 | |
| 3tgp | GNP | GTPase HRas | / | 0.655 | |
| 4epx | GDP | GTPase KRas | / | 0.655 | |
| 1ayl | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.654 | |
| 2jj1 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.654 | |
| 3oa2 | NAD | UDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase | / | 0.654 | |
| 3vc1 | SAH | Geranyl diphosphate 2-C-methyltransferase | 2.1.1.255 | 0.653 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.653 | |
| 4ymu | ATP | ABC-type polar amino acid transport system, ATPase component | / | 0.653 | |
| 1fmw | ATP | Myosin-2 heavy chain | / | 0.652 | |
| 1lfd | GNP | GTPase HRas | / | 0.652 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.652 | |
| 1xmv | ADP | Protein RecA | / | 0.651 | |
| 2w2x | GSP | Ras-related C3 botulinum toxin substrate 2 | / | 0.651 | |
| 3bbp | GTP | Ras-related protein Rab-6A | / | 0.651 | |
| 1h8h | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.650 | |
| 1h8h | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.650 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.650 | |
| 2r9v | ATP | ATP synthase subunit alpha | / | 0.650 | |
| 2x2r | ADP | Kinesin-like protein KIF11 | / | 0.650 | |
| 4qbi | AP5 | Adenylate kinase | / | 0.650 | |
| 4wa7 | GDP | GTPase KRas | / | 0.650 |