Structure of PDB 8yq8 Chain A Binding Site BS03

Receptor Information

>8yq8 Chain A (length=524) Species: 478864 (Plasmodium falciparum VS/1)

EQVCDVFDIYAICACCKVESEVFNNYTFRGLGNKGVLPWKCISLDMKYFR
AVTTYVNESKYEKLKYKRCKYLNKLQNVVVMGRTNWESIPKKFKPLSNRI
NVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGGSVVYQEF
LEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDF
IIYKKTDDEEEDDFVYFNFNKKNSIHPNDFQIYNSLKYKYHPEYQYLNII
YDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEE
LLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGF
QWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDL
DQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMI
AQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKN
IEDFTISDFTIQNYVHHEKISMDM

Ligand information

• Ligand ID: UMP
• InChI: InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: JSRLJPSBLDHEIO-SHYZEUOFSA-N
• SMILES:
  ACDLabs 12.01: O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
  CACTVS 3.370: O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
  CACTVS 3.370: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
• Formula: C9 H13 N2 O8 P
• Name: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
  DUMP
• ChEMBL: CHEMBL211312
• DrugBank: DB03800
• ZINC: ZINC000004228260
• PDB chain: 8yq8 Chain A Residue 703

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yq8 Novel flexible biphenyl Pf DHFR inhibitors with improved antimalarial activity.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): R345 C490 H491 Q509 R510 S511 D513 N521 H551 Y553
• Binding residue (residue number reindexed from 1): R263 C408 H409 Q427 R428 S429 D431 N439 H469 Y471
• Annotation score: 3

External links

• PDB: RCSB:8yq8, PDBe:8yq8, PDBj:8yq8
• PDBsum: 8yq8
• PubMed: 39026651
• UniProt: D9N170