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 |
|---|---|---|---|
| 4prx | ADP | DNA gyrase subunit B |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4prx | ADP | DNA gyrase subunit B | / | 1.097 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.986 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.958 | |
| 4wuc | ANP | DNA gyrase subunit B | / | 0.913 | |
| 1s16 | ANP | DNA topoisomerase 4 subunit B | / | 0.886 | |
| 3zkb | ANP | DNA gyrase subunit B | / | 0.864 | |
| 1z5c | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.833 | |
| 1z5a | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.825 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.802 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.798 | |
| 3zkd | ANP | DNA gyrase subunit B | / | 0.796 | |
| 1th8 | ADP | Anti-sigma F factor | / | 0.795 | |
| 2zkj | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.791 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.789 | |
| 2xcm | ADP | Cytosolic heat shock protein 90 | / | 0.767 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.759 | |
| 1mx0 | ANP | Type 2 DNA topoisomerase 6 subunit B | / | 0.753 | |
| 1ei1 | ANP | DNA gyrase subunit B | / | 0.752 | |
| 3t2s | AGS | Heat shock protein HSP 90-alpha | / | 0.751 | |
| 4gqt | ADP | Heat shock protein 90 | / | 0.750 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.742 | |
| 4gt8 | ADP | Sensor protein VraS | 2.7.13.3 | 0.742 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.728 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.727 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.725 | |
| 3t1k | ANP | Heat shock protein HSP 90-alpha | / | 0.721 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.717 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.714 | |
| 3t10 | ACP | Heat shock protein HSP 90-alpha | / | 0.712 | |
| 4ivg | ANP | TNF receptor-associated protein 1 | / | 0.710 | |
| 4xcl | AGS | Heat shock cognate 90 kDa protein | / | 0.708 | |
| 2c2a | ADP | Sensor histidine kinase | / | 0.704 | |
| 3t0z | ATP | Heat shock protein HSP 90-alpha | / | 0.703 | |
| 2ior | ADP | Chaperone protein HtpG | / | 0.695 | |
| 4r39 | ANP | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.695 | |
| 1z59 | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.694 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.693 | |
| 4xc0 | ACP | Heat shock cognate 90 kDa protein | / | 0.692 | |
| 4bix | ADP | Sensor histidine kinase CpxA | / | 0.691 | |
| 3h4l | ANP | DNA mismatch repair protein PMS1 | / | 0.689 | |
| 1zxn | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.688 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.687 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.683 | |
| 1i58 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.682 | |
| 1id0 | ANP | Sensor protein PhoQ | 2.7.13.3 | 0.681 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.677 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.676 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.673 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.668 | |
| 2yef | ANP | Heat shock protein HSP 90-alpha | / | 0.666 | |
| 2xk2 | ADP | Heat shock protein HSP 90-alpha | / | 0.665 | |
| 3dge | ADP | Sensor histidine kinase | / | 0.665 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.665 | |
| 4xcj | ADP | Heat shock cognate 90 kDa protein | / | 0.665 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.663 | |
| 3ehj | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.663 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.662 | |
| 5f5r | ANP | Heat shock protein 75 kDa, mitochondrial | / | 0.661 | |
| 5c93 | ACP | Two-component system histidine protein kinase | / | 0.660 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.659 | |
| 4p5a | FAD | Flavin-dependent thymidylate synthase | / | 0.659 | |
| 1am1 | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.658 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.658 | |
| 3bbd | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.657 | |
| 2ido | TMP | DNA polymerase III subunit epsilon | 2.7.7.7 | 0.655 | |
| 5ce3 | ADP | Protein kinase YopO | / | 0.655 | |
| 1kh2 | ATP | Argininosuccinate synthase | / | 0.654 | |
| 4biz | ADP | Sensor histidine kinase CpxA | / | 0.654 | |
| 4zol | ACP | Tubulin tyrosine ligase | / | 0.653 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.652 | |
| 3cr3 | ADP | PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.652 | |
| 4fl2 | ANP | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.652 | |
| 1s4d | SAH | Uroporphyrinogen-III C-methyltransferase | 2.1.1.107 | 0.651 | |
| 3a5y | KAA | Elongation factor P--(R)-beta-lysine ligase | / | 0.651 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.651 | |
| 3ryp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.651 | |
| 1fyf | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.650 | |
| 1l0o | ADP | Anti-sigma F factor | / | 0.650 |