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 |
|---|---|---|---|
| 3bbd | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3bbd | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 1.060 | |
| 4fak | SAM | Ribosomal RNA large subunit methyltransferase H | / | 0.788 | |
| 3bbh | SFG | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.787 | |
| 2qmm | SAM | tRNA (pseudouridine(54)-N(1))-methyltransferase | / | 0.768 | |
| 3oii | SAH | Ribosomal RNA small subunit methyltransferase NEP1 | / | 0.763 | |
| 2egw | SAH | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | 0.758 | |
| 2egv | SAM | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | 0.746 | |
| 4cnf | MTA | SpoU rRNA methylase | / | 0.741 | |
| 4cng | SAH | SpoU rRNA methylase | / | 0.737 | |
| 3oij | SAH | Ribosomal RNA small subunit methyltransferase NEP1 | / | 0.736 | |
| 4pzk | SAH | Putative tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.732 | |
| 3o7b | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | / | 0.730 | |
| 5a7y | SAH | tRNA (adenine(9)-N1)-methyltransferase | 2.1.1.218 | 0.728 | |
| 4jwj | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.723 | |
| 2cx8 | SAH | Ribosomal RNA small subunit methyltransferase E | / | 0.711 | |
| 4jwh | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.706 | |
| 2ha8 | SAH | Probable methyltransferase TARBP1 | / | 0.702 | |
| 2yy8 | MTA | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.701 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.696 | |
| 4x3l | MTA | RNA 2'-O ribose methyltransferase | / | 0.692 | |
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.689 | |
| 3nk7 | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.686 | |
| 4kgn | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.680 | |
| 1mjh | ATP | Universal stress protein MJ0577 | / | 0.678 | |
| 2z08 | ATP | Universal stress protein family | / | 0.676 | |
| 1v3s | ATP | Signaling protein | / | 0.673 | |
| 2ybo | SAH | Methyltransferase | / | 0.673 | |
| 4h3y | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.673 | |
| 3hgm | ATP | TRAP-T-associated universal stress protein TeaD | / | 0.672 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.671 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.669 | |
| 3n4k | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.669 | |
| 4jal | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.669 | |
| 2yy8 | SAM | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.668 | |
| 4jlp | ADP | Adenylate kinase | / | 0.668 | |
| 1vp6 | CMP | Cyclic nucleotide-gated potassium channel mll3241 | / | 0.664 | |
| 3vpc | ADP | Glutamate--LysW ligase ArgX | 6.3.2 | 0.664 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.663 | |
| 4co4 | ATP | Nitrogen regulatory protein P-II 1 | / | 0.663 | |
| 3tw6 | ADP | Pyruvate carboxylase | / | 0.660 | |
| 4yvh | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.660 | |
| 4yvj | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.658 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.657 | |
| 4yvk | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.657 | |
| 4hbn | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.656 | |
| 4i01 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.656 | |
| 4i0b | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.655 | |
| 1cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.654 | |
| 1ne6 | SP1 | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.654 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.654 | |
| 3wnz | ADP | Alanine--anticapsin ligase | / | 0.654 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.654 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.653 | |
| 2ioa | ADP | Bifunctional glutathionylspermidine synthetase/amidase | / | 0.652 | |
| 2r7n | ADP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.652 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.651 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.651 | |
| 3vpb | ADP | Glutamate--LysW ligase ArgX | 6.3.2 | 0.650 | |
| 4x3m | ADN | RNA 2'-O ribose methyltransferase | / | 0.650 |