File:Nucleotides syn1.svg

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Summary

Description
English: The synthesis of IMP. The color scheme is as follows: enzymes, coenzymes, substrate names, metal ions, inorganic molecules .
Image created using LaTeX and the generated PDF converted to SVG using this.
Date
Source Own work
Author Krishnavedala
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Source code
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LaTeX code

Source code
\documentclass[12pt,border=1pt]{standalone}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{chemfig,chemmacros}
\usepackage{lmodern}
\usetikzlibrary{decorations.pathmorphing}

\chemsetup[chemformula]{font-shape=sf,format=\sffamily}
\renewcommand*{\familydefault}{\sfdefault}
\renewcommand*\printatom[1]{\ensuremath{\mathsf{#1} } }
\setatomsep{2.5em}
\setdoublesep{.6ex}
\setarrowdefault{,2,thick}
\setbondstyle{thick}

\makeatletter
% From: http://tex.stackexchange.com/a/125761
% Initial arguments:
% #1, #2: Same as for -U> (above arrow)
% #3: Additional label at midpoint (also above arrow)
% #4, #5, #6: Like #1, #2, and #3, but below arrow
\definearrow9{-X>}{%
    \CF@arrow@shift@nodes{#7}%
    \expandafter\draw\expandafter[\CF@arrow@current@style,-CF@full](\CF@arrow@start@node)--(\CF@arrow@end@node)node[midway](Xarrow@arctangent){};%
    \edef\CF@tmp@str{\ifx\@empty#1\@empty[draw=none]\fi}%
    \expandafter\draw\CF@tmp@str (Xarrow@arctangent)%
        arc[radius=\CF@compound@sep*\CF@current@arrow@length*\ifx\@empty#8\@empty0.333\else#8\fi,start angle=\CF@arrow@current@angle-90,%
        delta angle=-\ifx\@empty#9\@empty60\else#9\fi]node(Xarrow1@start){};
    \edef\CF@tmp@str{[\ifx\@empty#2\@empty draw=none,\fi-CF@full]}%
    \expandafter\draw\CF@tmp@str (Xarrow@arctangent)%
        arc[radius=\CF@compound@sep*\CF@current@arrow@length*\ifx\@empty#8\@empty0.333\else#8\fi,start angle=\CF@arrow@current@angle-90,%
        delta angle=\ifx\@empty#9\@empty60\else#9\fi]node(Xarrow1@end){};
    \edef\CF@tmp@str{\ifx\@empty#4\@empty[draw=none]\fi}%
    \expandafter\draw\CF@tmp@str (Xarrow@arctangent)%
        arc[radius=\CF@compound@sep*\CF@current@arrow@length*\ifx\@empty#8\@empty0.333\else#8\fi,start angle=\CF@arrow@current@angle+90,%
        delta angle=\ifx\@empty#9\@empty60\else#9\fi]node(Xarrow2@start){};
    \edef\CF@tmp@str{[\ifx\@empty#5\@empty draw=none,\fi-CF@full]}%
    \expandafter\draw\CF@tmp@str (Xarrow@arctangent)%
        arc[radius=\CF@compound@sep*\CF@current@arrow@length*\ifx\@empty#8\@empty0.333\else#8\fi,start angle=\CF@arrow@current@angle+90,%
        delta angle=-\ifx\@empty#9\@empty60\else#9\fi]node(Xarrow2@end){};
    \edef\CF@tmp@str{\if\string-\expandafter\@car\detokenize{#7.}\@nil-\else+\fi}%
    \CF@arrow@display@label{#1}{0}\CF@tmp@str{Xarrow1@start}{#2}{1}\CF@tmp@str{Xarrow1@end}%
    \CF@arrow@display@label{#3}{0.5}\CF@tmp@str\CF@arrow@start@node{}{}{}\CF@arrow@end@node%
    \edef\CF@tmp@str{\if\string-\expandafter\@car\detokenize{#7.}\@nil+\else-\fi}%
    \CF@arrow@display@label{#4}{0}\CF@tmp@str{Xarrow2@start}{#5}{1}\CF@tmp@str{Xarrow2@end}%
    \CF@arrow@display@label{#6}{0.5}\CF@tmp@str\CF@arrow@start@node{}{}{}\CF@arrow@end@node%
}
\makeatother

\begin{document}
\definesubmol\nobond{-[,0.2,,,draw=none]}
\definesubmol{rb}{Ribotide}
\schemestart[][west]
	\chemname{\chemfig{ {\color{red}P}-O--[:-18]*5(-(<:HO)-(<:OH)-(<:OH)-O-) } }{\color{brown}R5P}
    \arrow{-X>[{\color{orange}ATP}][{\color{orange}AMP}][{\color{magenta}\ch{Mg^2+} }][][][\color{blue}PRPS1]}
	\chemname{\chemfig{ {\color{red}P}-O--[:-18]*5(-(<:HO)-(<:OH)-(<:O-[0]{\color{red}P}-[0,,,,red,decorate,decoration=snake, segment length=6pt]{ {\color{red}P} })-O-) } }{\color{brown}PRPP}
    \arrow{-X>[{\color{orange}Gln},{\color{red}\ch{H2O} }][{\color{brown}Glu},{\color{red}2\ch{P_i} }][{\color{magenta}\ch{Mg^2+} }][][][\parbox{5em}{\centering\color{blue}PPAT\\1}]}
    \chemname{\chemfig{ {\color{red}P}-O--[:-18]*5(-(<:HO)-(<:OH)-(<NH_2)-O-) } }{\color{brown}5-PRA}
    \arrow(.-45--){-X>[*0{ {\color{orange}ATP},{\color{brown}Gly} }][*0{ {\color{orange}ADP},{\color{red}\ch{P_i} } }][*0{\color{magenta}\ch{Mg^2+} }][][][*0\parbox{5em}{\centering\color{blue}GART (E1)\\2}]}[-90,1.5]
    \chemname*{\chemfig{O=[:30](-[2]-[::-60]NH_2)-[:-30]NH-[6,,1]!{rb} } }{\color{brown}GAR}
    \arrow{-X>[][][\parbox{5em}{\centering\color{blue}GART (E2)\\3}][\parbox{2.75cm}{ {\color{orange}\ch{N^{10} }-formyl-THF} }][{\color{orange}THF}][][-2em]}[180,3]
    \chemname*{\chemfig{ O=[:30] *6(-NH(-[6]!{rb})-[,,,,draw=none]O=-NH--) } }{\color{brown}FGAR}
    \arrow{-X>[][][\parbox{5em}{\centering\color{blue}PFAS\\4}][{\color{orange}Gln},{\color{orange}ATP},{\color{red}\ch{H2O} }][{\color{brown}Glu},{\color{orange}ADP},{\color{red}\ch{P_i} }][{\color{magenta}\ch{Mg^2+} }][-2em]}[180,2.5]
    \chemname*{\chemfig{ HN=[:30] *6(-NH(-[6]!{rb})-[,,,,draw=none]O=-NH--) } }{\color{brown}FGAM}
    \arrow{-X>[][][\parbox{5em}{\centering\color{blue}GART (E3)\\5}][{\color{orange}ATP}][{\color{orange}ADP},{\color{red}\ch{P_i} }][{\color{magenta}\ch{Mg^2+} }][-2em]}[180]
    \chemname*{\chemfig{*5((-H_2N)-N(-!{rb})-=N-=)} }{\color{brown}AIR}
    \arrow{-X>[*0{ {\color{orange}ATP},{\color{red}\ch{HCO3^-} } }][*0{ {\color{orange}ADP},{\color{red}\ch{P_i} } }][*0{\color{magenta}\ch{Mg^2+} }][][][*0\parbox{5em}{\centering\color{blue}PAICS (E1)\\6}]}[-90]
    \chemname*{\chemfig{*5((-HN_2)-N(-!{rb}) -=N- (-[:150](=[::-60]O)-[::60]OH) =)} }{\color{brown}CAIR}
    \arrow{-X>[{\color{orange}ATP},{\color{brown}ASP}][{\color{orange}ADP},{\color{red}\ch{P_i} }][{\color{magenta}\ch{Mg^2+} }][][][\parbox{5em}{\centering\color{blue}PAICS (E2)\\7}]}
    \chemname*{\chemfig{ O=[:30] *6(-O^{-} -[,,,,draw=none]-[,,,,draw=none]\chembelow{N}{H} (-[:30](=[2]O)-[:-36]*5(=(-H_2N)-N(-!{rb})-=N-))
    	- (-(=[::60]O)-[::-60]O^{-}) --) } }{\color{brown}SACAIR}
    \arrow{-X>[][{\color{brown}Fumarate}][][][][\parbox{5em}{\centering\color{blue}ADSL\\8}]}\quad
    \chemname*{\chemfig{*5((-HN_2)-N(-!{rb}) -=N- (-[:120](=[::-60]O)-[::60]NH_2) =)} }{\color{brown}AICAR}
    \arrow(.-50--){-X>[*0\parbox{2.75cm}{ {\color{orange}\ch{N^{10} }-formyl-THF} }][*0{ {\color{orange}THF} } ][][][][*0\parbox{5em}{\centering\color{blue}ATIC (E1)\\9}]}[-90,1.5]
    \chemname*{\chemfig{*5((-HN-[::-60]=[::60]O)-N(-!{rb}) -=N- (-[:150](=[::-60]O)-[::60]NH_2) =)} }{\color{brown}FAICAR}
    \arrow{-X>[][][\parbox{5em}{\centering\color{blue}ATIC (E2)\\10}][][{\color{red}\ch{H2O} }][][-2em]}[180,2.5]
    \chemname*{\chemfig{ *6(=N- (*5(-N(-!{rb})-=N-=)) --(=O) -[,,,2]HN-[,,2]=) } }{\color{brown}IMP}
\schemestop
\end{document}

Licensing

I, the copyright holder of this work, hereby publish it under the following license:
Creative Commons CC-Zero This file is made available under the Creative Commons CC0 1.0 Universal Public Domain Dedication.
The person who associated a work with this deed has dedicated the work to the public domain by waiving all of their rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.

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6 August 2014

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current19:48, 6 August 2014Thumbnail for version as of 19:48, 6 August 20141,062 × 958 (129 KB)Krishnavedala{{Information |Description ={{en|1=The synthesis of IMP. The color scheme is as follows: <span style="font-weight: bold;"><span style="color: blue;">enzymes</span>, <span style="color: orange">coenzymes</span>, <span style="color: brown;">substrate...
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