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 |
|---|---|---|---|
| 2egw | SAH | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2egw | SAH | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | 1.061 | |
| 2egv | SAM | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | 0.882 | |
| 2cx8 | SAH | Ribosomal RNA small subunit methyltransferase E | / | 0.773 | |
| 3bbd | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.758 | |
| 4fak | SAM | Ribosomal RNA large subunit methyltransferase H | / | 0.747 | |
| 3oii | SAH | Ribosomal RNA small subunit methyltransferase NEP1 | / | 0.739 | |
| 3o7b | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | / | 0.738 | |
| 4pzk | SAH | Putative tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.735 | |
| 3n4k | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.733 | |
| 2ha8 | SAH | Probable methyltransferase TARBP1 | / | 0.731 | |
| 4x3l | MTA | RNA 2'-O ribose methyltransferase | / | 0.729 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.713 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.710 | |
| 4cnf | MTA | SpoU rRNA methylase | / | 0.703 | |
| 2eka | SAH | Diphthine synthase | / | 0.702 | |
| 4kgn | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.699 | |
| 4cng | SAH | SpoU rRNA methylase | / | 0.695 | |
| 2ybo | SAH | Methyltransferase | / | 0.694 | |
| 3rk1 | ATP | N-type ATP pyrophosphatase superfamily | / | 0.692 | |
| 2qmm | SAM | tRNA (pseudouridine(54)-N(1))-methyltransferase | / | 0.691 | |
| 3oij | SAH | Ribosomal RNA small subunit methyltransferase NEP1 | / | 0.691 | |
| 3bbh | SFG | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.689 | |
| 1s4d | SAH | Uroporphyrinogen-III C-methyltransferase | 2.1.1.107 | 0.688 | |
| 3gyq | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.688 | |
| 1kh2 | ATP | Argininosuccinate synthase | / | 0.687 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.685 | |
| 2z08 | ATP | Universal stress protein family | / | 0.684 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.683 | |
| 5a7y | SAH | tRNA (adenine(9)-N1)-methyltransferase | 2.1.1.218 | 0.681 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.680 | |
| 3hgm | ATP | TRAP-T-associated universal stress protein TeaD | / | 0.680 | |
| 4h3z | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.680 | |
| 1cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.679 | |
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.679 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.677 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.677 | |
| 2ioa | ADP | Bifunctional glutathionylspermidine synthetase/amidase | / | 0.676 | |
| 2xul | ATP | Nitrogen regulatory protein P-II | / | 0.676 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.675 | |
| 4jal | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.673 | |
| 2z6r | SAH | Diphthine synthase | / | 0.672 | |
| 2dxv | SAH | Diphthine synthase | / | 0.671 | |
| 2dxx | SAH | Diphthine synthase | / | 0.671 | |
| 2ehl | SAH | Diphthine synthase | / | 0.671 | |
| 4jwj | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.671 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.671 | |
| 5ahw | CMP | Universal stress protein family protein, putative | / | 0.668 | |
| 2yy8 | MTA | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.665 | |
| 1v3s | ATP | Signaling protein | / | 0.664 | |
| 4jlp | ADP | Adenylate kinase | / | 0.663 | |
| 2e07 | SAH | Diphthine synthase | / | 0.662 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.661 | |
| 2e7r | SAH | Diphthine synthase | / | 0.661 | |
| 2egb | SAH | Diphthine synthase | / | 0.661 | |
| 2egl | SAH | Diphthine synthase | / | 0.661 | |
| 2en5 | SAH | Diphthine synthase | / | 0.661 | |
| 2yy8 | SAM | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.661 | |
| 2z0y | SAM | Ribosomal RNA small subunit methyltransferase E | / | 0.661 | |
| 3vpc | ADP | Glutamate--LysW ligase ArgX | 6.3.2 | 0.661 | |
| 2dsg | SAH | Diphthine synthase | / | 0.660 | |
| 2e08 | SAH | Diphthine synthase | / | 0.660 | |
| 1s16 | ANP | DNA topoisomerase 4 subunit B | / | 0.659 | |
| 1v9o | ADP | Signaling protein | / | 0.659 | |
| 2dsh | SAH | Diphthine synthase | / | 0.659 | |
| 3vpb | ADP | Glutamate--LysW ligase ArgX | 6.3.2 | 0.659 | |
| 1mjh | ATP | Universal stress protein MJ0577 | / | 0.655 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.655 | |
| 2egs | SAH | Diphthine synthase | / | 0.655 | |
| 3s3t | ATP | Universal stress protein | / | 0.655 | |
| 4h3y | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.655 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.654 | |
| 2p5c | SAH | Diphthine synthase | / | 0.654 | |
| 2ptm | CMP | Hyperpolarization-activated (Ih) channel | / | 0.653 | |
| 4x3m | ADN | RNA 2'-O ribose methyltransferase | / | 0.653 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.652 | |
| 2hut | SAH | Diphthine synthase | / | 0.652 | |
| 4ffm | ADP | Uncharacterized protein | / | 0.652 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.652 | |
| 2pca | SAH | Diphthine synthase | / | 0.651 | |
| 2pck | SAH | Diphthine synthase | / | 0.651 | |
| 2e15 | SAH | Diphthine synthase | / | 0.650 | |
| 2e17 | SAH | Diphthine synthase | / | 0.650 | |
| 2emr | SAH | Diphthine synthase | / | 0.650 | |
| 2p6i | SAH | Diphthine synthase | / | 0.650 | |
| 4jl8 | ADP | Adenylate kinase | / | 0.650 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.650 |