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 |
|---|---|---|---|
| 4wud | ANP | DNA gyrase subunit B |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4wud | ANP | DNA gyrase subunit B | / | 1.202 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 1.149 | |
| 3zkb | ANP | DNA gyrase subunit B | / | 1.010 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.958 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.952 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.943 | |
| 1mx0 | ANP | Type 2 DNA topoisomerase 6 subunit B | / | 0.929 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.909 | |
| 3zkd | ANP | DNA gyrase subunit B | / | 0.906 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.860 | |
| 4ipe | ANP | TNF receptor-associated protein 1 | / | 0.855 | |
| 1ei1 | ANP | DNA gyrase subunit B | / | 0.853 | |
| 1s16 | ANP | DNA topoisomerase 4 subunit B | / | 0.853 | |
| 4ivg | ANP | TNF receptor-associated protein 1 | / | 0.843 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.810 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.800 | |
| 1z5a | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.790 | |
| 1z5c | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.781 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.771 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.765 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.761 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.760 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.758 | |
| 1th8 | ADP | Anti-sigma F factor | / | 0.755 | |
| 3t0z | ATP | Heat shock protein HSP 90-alpha | / | 0.755 | |
| 3h4l | ANP | DNA mismatch repair protein PMS1 | / | 0.752 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.749 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.743 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.740 | |
| 1byq | ADP | Heat shock protein HSP 90-alpha | / | 0.737 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.737 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.737 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.732 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.724 | |
| 4r39 | ANP | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.724 | |
| 3kmw | ATP | Integrin-linked protein kinase | 2.7.11.1 | 0.717 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.715 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.714 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.710 | |
| 4biw | ANP | Sensor histidine kinase CpxA | / | 0.708 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.708 | |
| 2ior | ADP | Chaperone protein HtpG | / | 0.701 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.701 | |
| 3rep | ATP | Integrin-linked protein kinase | 2.7.11.1 | 0.697 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.696 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.694 | |
| 1xje | GDP | Vitamin B12-dependent ribonucleotide reductase | / | 0.687 | |
| 1z59 | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.687 | |
| 2o1u | ANP | Endoplasmin | / | 0.684 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.684 | |
| 4gt8 | ADP | Sensor protein VraS | 2.7.13.3 | 0.684 | |
| 3dge | ADP | Sensor histidine kinase | / | 0.674 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.674 | |
| 4a61 | ANP | Plasmid segregation protein ParM | / | 0.670 | |
| 4m69 | ANP | Receptor-interacting serine/threonine-protein kinase 3 | 2.7.11.1 | 0.667 | |
| 2ido | TMP | DNA polymerase III subunit epsilon | 2.7.7.7 | 0.666 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.666 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.662 | |
| 2pz8 | APC | NH(3)-dependent NAD(+) synthetase | / | 0.661 | |
| 5cno | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.660 | |
| 1ih8 | APC | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.657 | |
| 5bsm | ATP | 4-coumarate--CoA ligase 2 | 6.2.1.12 | 0.657 | |
| 4r8h | SP1 | cAMP-activated global transcriptional regulator CRP | / | 0.656 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.655 | |
| 1n75 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.654 | |
| 2v9x | DUT | dCTP deaminase | / | 0.654 | |
| 3akd | CDP | Cytidylate kinase | / | 0.653 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.653 | |
| 2qcs | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.652 | |
| 2dsc | APR | ADP-sugar pyrophosphatase | 3.6.1.13 | 0.651 | |
| 4i0b | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.651 | |
| 3lmg | ANP | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.650 | |
| 3ruv | ANP | Chaperonin | / | 0.650 | |
| 4col | DTP | Uncharacterized protein | / | 0.650 | |
| 4dh7 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.650 |