Structure based on 5jlx

Ideal structure
Name: 2'-deoxy-5'-o-thiophosphonocytidine
Formula: C9 H14 N3 O6 P S
Weight: 323.263
SMILES: "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2"
Spacial conformation based on PDB 5jlx.
Also present on 6w3u
RESIDUE   C7S     34
CONECT      P      4 O5'  SP1  OP2  OP3 
CONECT      C5'    4 O5'  C4'  H1   H2  
CONECT      O5'    2 P    C5' 
CONECT      C4'    4 C5'  O4'  C3'  H3  
CONECT      O4'    2 C4'  C1' 
CONECT      C3'    4 C4'  O3'  C2'  H4  
CONECT      O3'    2 C3'  H5  
CONECT      C2'    4 C3'  C1'  H6   H7  
CONECT      C1'    4 O4'  C2'  N1   H8  
CONECT      N1     3 C1'  C2   C6  
CONECT      C2     3 N1   O2   N3  
CONECT      O2     1 C2  
CONECT      N3     2 C2   C4  
CONECT      C4     3 N3   N4   C5  
CONECT      N4     3 C4   H9   H10 
CONECT      C5     3 C4   C6   H11 
CONECT      C6     3 N1   C5   H12 
CONECT      SP1    2 P    HSP1
CONECT      OP2    1 P   
CONECT      OP3    2 P    HOP3
CONECT      H1     1 C5' 
CONECT      H2     1 C5' 
CONECT      H3     1 C4' 
CONECT      H4     1 C3' 
CONECT      H5     1 O3' 
CONECT      H6     1 C2' 
CONECT      H7     1 C2' 
CONECT      H8     1 C1' 
CONECT      H9     1 N4  
CONECT      H10    1 N4  
CONECT      H11    1 C5  
CONECT      H12    1 C6  
CONECT      HSP1   1 SP1 
CONECT      HOP3   1 OP3 
END   
HET    C7S             34
HETSYN     C7S 2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connec
HETSYN   2 C7S tion isoform 2)
HETNAM     C7S 2'-deoxy-5'-O-thiophosphonocytidine
FORMUL      C7S    C9 H14 N3 O6 P1 S1

This OCA MONOMER page
uses Jmol, developed by the Jmol Development Team (color reference)
OCA© by Jaime Prilusky, 1996-2004,2006,2010,2014
Bioinformatics Unit
Weizmann Institute of Science