Structure of PDB 8vph Chain B Binding Site BS03

Receptor Information

>8vph Chain B (length=551) Species: 1496 (Clostridioides difficile)

SGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDIL
YDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDS
LTNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEK
KYKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESL
SGKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYID
VFKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETF
YNKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCW
IKSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRE
CKSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVY
SFFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVM
KIRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLG
I

Ligand information

• Ligand ID: Q8Y
• InChI: InChI=1S/C19H23N5O4/c25-9-13-15(26)16(27)19(28-13)24-11-23-14-17(21-10-22-18(14)24)20-8-4-7-12-5-2-1-3-6-12/h1-3,5-6,10-11,13,15-16,19,25-27H,4,7-9H2,(H,20,21,22)/t13-,15-,16-,19-/m1/s1
• InChIKey: UBRRRMDHTZACMR-NVQRDWNXSA-N
• SMILES:
  ACDLabs 12.01: OCC1OC(n2cnc3c(NCCCc4ccccc4)ncnc32)C(O)C1O
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CCCNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O
  CACTVS 3.385: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCCCc4ccccc4)ncnc23
  CACTVS 3.385: OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(NCCCc4ccccc4)ncnc23
• Formula: C19 H23 N5 O4
• Name: N-(3-phenylpropyl)adenosine
• ChEMBL: CHEMBL2113484
• PDB chain: 8vph Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vph Quinoline-based compounds can inhibit diverse enzymes that act on DNA
• Resolution: 3.18 Å
• Binding residue (original residue number in PDB): I61 D114 I115 D149 S150 P167 Y178 F200
• Binding residue (residue number reindexed from 1): I35 D88 I89 D123 S124 P141 Y152 F174
• Annotation score: 1

External links

• PDB: RCSB:8vph, PDBe:8vph, PDBj:8vph
• PDBsum: 8vph
• UniProt: A0A031WG99