Structure based on 5jlw

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 5jlw.
Also present on 5u9h
RESIDUE   C7R     34
CONECT      P      4 O5'  OP1  SP2  OP3 
CONECT      C5'    4 O5'  C4'  H5'2 H5'1
CONECT      O5'    2 P    C5' 
CONECT      C4'    4 C5'  O4'  C3'  H4' 
CONECT      O4'    2 C4'  C1' 
CONECT      C3'    4 C4'  O3'  C2'  H3' 
CONECT      O3'    2 C3'  H1  
CONECT      C2'    4 C3'  C1'  H2'1 H2'2
CONECT      C1'    4 O4'  C2'  N1   H1' 
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   H42  H41 
CONECT      C5     3 C4   C6   H5  
CONECT      C6     3 N1   C5   H6  
CONECT      OP1    1 P   
CONECT      SP2    2 P    HSP2
CONECT      OP3    2 P    HOP3
CONECT      H5'2   1 C5' 
CONECT      H5'1   1 C5' 
CONECT      H4'    1 C4' 
CONECT      H3'    1 C3' 
CONECT      H1     1 O3' 
CONECT      H2'1   1 C2' 
CONECT      H2'2   1 C2' 
CONECT      H1'    1 C1' 
CONECT      H42    1 N4  
CONECT      H41    1 N4  
CONECT      H5     1 C5  
CONECT      H6     1 C6  
CONECT      HSP2   1 SP2 
CONECT      HOP3   1 OP3 
END   
HET    C7R             34
HETSYN     C7R 2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connec
HETSYN   2 C7R tion isoform 1)
HETNAM     C7R 2'-deoxy-5'-O-thiophosphonocytidine
FORMUL      C7R    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