Structure of PDB 7dm5 Chain D Binding Site BS02

Receptor Information

>7dm5 Chain D (length=157) Species: 3702 (Arabidopsis thaliana)

SDHKFLTQAVEEAYKGVDCGDGGPFGAVIVHNNEVVASCHNMVLKYTDPT
AHAEVTAIREACKKLNKIELSECEIYASCEPCPMCFGAIHLSRLKRLVYG
AKAEAAIAIGFDDFIADALRGTGVYQKSSLEIKKADGNGAAIAEQVFQNT
KEKFRLY

Ligand information

• Ligand ID: 4UO
• InChI: InChI=1S/C10H12N4O6/c15-1-3-5(16)6(17)9(20-3)14-2-11-4-7(14)12-10(19)13-8(4)18/h2-3,5-6,9,15-17H,1H2,(H2,12,13,18,19)/t3-,5-,6-,9-/m1/s1
• InChIKey: UBORTCNDUKBEOP-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1nc2c(n1C3C(C(C(O3)CO)O)O)NC(=O)NC2=O
  ACDLabs 12.01: O=C1NC(=O)Nc2c1ncn2C3C(C(C(O3)CO)O)O
  OpenEye OEToolkits 1.9.2: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)NC(=O)NC2=O
  CACTVS 3.385: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=O)Nc23
  CACTVS 3.385: OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)NC(=O)Nc23
• Formula: C10 H12 N4 O6
• Name: 2,3-dihydroxanthosine;
  Xanthosine
• ChEMBL: CHEMBL402439
• ZINC: ZINC000001561970
• PDB chain: 7dm5 Chain D Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7dm5 Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): F53 N69 H80 E82 P109 C110 C113 F139 D140 F142 Y185
• Binding residue (residue number reindexed from 1): F25 N41 H52 E54 P81 C82 C85 F111 D112 F114 Y157
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.5.4.15: guanosine deaminase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity

External links

• PDB: RCSB:7dm5, PDBe:7dm5, PDBj:7dm5
• PDBsum: 7dm5
• PubMed: 36499303
• UniProt: Q94BU8|GSDA_ARATH Guanosine deaminase (Gene Name=GSDA)