7Y4K
Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-ornitine
Summary for 7Y4K
| Entry DOI | 10.2210/pdb7y4k/pdb |
| Descriptor | Ricin A chain, (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-5-(phenylmethoxycarbonylamino)pentanoic acid, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | hydrolase inhibitor, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor |
| Biological source | Ricinus communis (castor bean) |
| Total number of polymer chains | 1 |
| Total formula weight | 31748.59 |
| Authors | Katakura, S.,Goto, M.,Ohba, T.,Kawata, R.,Nagatsu, K.,Higashi, S.,Matsumoto, K.,Kurisu, K.,Ohtsuka, K.,Saito, R. (deposition date: 2022-06-15, release date: 2022-11-16, Last modification date: 2023-11-29) |
| Primary citation | Saito, R.,Goto, M.,Katakura, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Higashi, S.,Kurisu, K.,Matsumoto, K.,Ohtsuka, K. Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain. Plos One, 17:e0277770-e0277770, 2022 Cited by PubMed Abstract: The Ricin toxin A chain (RTA), which depurinates an adenine base at a specific region of the ribosome leading to death, has two adjacent specificity pockets in its active site. Based on this structural information, many attempts have been made to develop small-molecule RTA inhibitors that simultaneously block the two pockets. However, no attempt has been successful. In the present study, we synthesized pterin-7-carboxamides with tripeptide pendants and found that one of them interacts with both pockets simultaneously to exhibit good RTA inhibitory activity. X-ray crystallographic analysis of the RTA crystal with the new inhibitor revealed that the conformational change of Tyr80 is an important factor that allows the inhibitors to plug the two pockets simultaneously. PubMed: 36508422DOI: 10.1371/journal.pone.0277770 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
Download full validation report
