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 |
|---|---|---|---|
| 2xul | ATP | Nitrogen regulatory protein P-II |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2xul | ATP | Nitrogen regulatory protein P-II | / | 1.266 | |
| 3mhy | ATP | Nitrogen regulatory protein P-II 1 | / | 1.124 | |
| 4aff | ATP | Nitrogen regulatory protein P-II | / | 0.922 | |
| 3ta2 | ATP | Nitrogen regulatory protein P-II (GlnB-3) | / | 0.779 | |
| 4fvq | ATP | Tyrosine-protein kinase JAK2 | / | 0.733 | |
| 4ozn | ATP | Ammonium transporter | / | 0.720 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.711 | |
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 0.708 | |
| 3ncq | ATP | Nitrogen regulatory protein P-II (GlnB-2) | / | 0.704 | |
| 2xzw | ATP | Nitrogen regulatory protein P-II | / | 0.701 | |
| 2v9x | DUT | dCTP deaminase | / | 0.698 | |
| 4usj | ATP | Nitrogen regulatory protein PII | / | 0.698 | |
| 2olq | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.697 | |
| 3ta0 | ATP | Nitrogen regulatory protein P-II (GlnB-3) | / | 0.696 | |
| 1xje | TTP | Vitamin B12-dependent ribonucleotide reductase | / | 0.693 | |
| 2wgh | DTP | Ribonucleoside-diphosphate reductase large subunit | 1.17.4.1 | 0.691 | |
| 4qnr | ATP | Psp operon transcriptional activator | / | 0.691 | |
| 2rgx | AP5 | Adenylate kinase | / | 0.690 | |
| 4fvr | ATP | Tyrosine-protein kinase JAK2 | / | 0.690 | |
| 1z2n | ADP | Inositol-tetrakisphosphate 1-kinase | 2.7.1.134 | 0.688 | |
| 5c03 | AGS | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.688 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.685 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.685 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.683 | |
| 3q1k | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.682 | |
| 2egv | SAM | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | 0.681 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.680 | |
| 2pz8 | APC | NH(3)-dependent NAD(+) synthetase | / | 0.677 | |
| 4yvz | 3AT | DNA integrity scanning protein DisA | / | 0.677 | |
| 2egw | SAH | Ribosomal RNA small subunit methyltransferase E | 2.1.1.193 | 0.676 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.676 | |
| 1r0z | ATP | Cystic fibrosis transmembrane conductance regulator | / | 0.675 | |
| 4qm6 | GTP | Metallophosphoesterase | / | 0.674 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.674 | |
| 1cjv | DAD | Adenylate cyclase type 2 | / | 0.673 | |
| 1cjv | DAD | Adenylate cyclase type 5 | / | 0.673 | |
| 3a58 | GNP | GTP-binding protein RHO1 | / | 0.668 | |
| 4f9a | ADP | Cell division cycle 7-related protein kinase | 2.7.11.1 | 0.668 | |
| 4tuy | GTP | Tubulin alpha-1B chain | / | 0.668 | |
| 5i4n | ATP | Tyrosine-protein kinase JAK2 | / | 0.668 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.666 | |
| 3lf0 | ATP | Nitrogen regulatory protein P-II | / | 0.665 | |
| 1w1w | AGS | Structural maintenance of chromosomes protein 1 | / | 0.664 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.664 | |
| 4tl7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.664 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.663 | |
| 1aq2 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.662 | |
| 4co4 | ATP | Nitrogen regulatory protein P-II 1 | / | 0.662 | |
| 4q4c | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.662 | |
| 1zc4 | GNP | Ras-related protein Ral-A | / | 0.661 | |
| 1ih8 | APC | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.660 | |
| 1v3s | ATP | Signaling protein | / | 0.660 | |
| 3s8a | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.660 | |
| 3wo0 | ADP | Alanine--anticapsin ligase | / | 0.660 | |
| 4cnf | MTA | SpoU rRNA methylase | / | 0.660 | |
| 4h5e | YS4 | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.660 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.659 | |
| 4mam | A12 | N5-carboxyaminoimidazole ribonucleotide synthase | / | 0.659 | |
| 1g17 | GNP | Ras-related protein SEC4 | / | 0.658 | |
| 2ywv | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | / | 0.658 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.657 | |
| 4cng | SAH | SpoU rRNA methylase | / | 0.657 | |
| 4nm7 | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.657 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.657 | |
| 1rj9 | GCP | Signal recognition particle receptor FtsY | / | 0.655 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.655 | |
| 1wa5 | GTP | GTP-binding nuclear protein Ran | / | 0.654 | |
| 3i12 | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.654 | |
| 2c5l | GTP | GTPase HRas | / | 0.653 | |
| 3wyf | GTP | GTP-binding nuclear protein | / | 0.653 | |
| 2r7n | ADP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.652 | |
| 1m7b | GTP | Rho-related GTP-binding protein RhoE | / | 0.650 | |
| 1p52 | ADP | Arginine kinase | 2.7.3.3 | 0.650 | |
| 1yv5 | RIS | Farnesyl pyrophosphate synthase | 2.5.1.10 | 0.650 | |
| 2cvx | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.650 | |
| 4ffb | GTP | Tubulin alpha-1 chain | / | 0.650 |