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Change structure of monomers #5111

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ljubica-milovic opened this issue Jul 16, 2024 · 1 comment · Fixed by #5619
Closed
20 tasks done

Change structure of monomers #5111

ljubica-milovic opened this issue Jul 16, 2024 · 1 comment · Fixed by #5619
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feature request Monomer Library
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Ketcher 2.26.0-rc.1

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@ljubica-milovic
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ljubica-milovic commented Jul 16, 2024 •
edited by AlexeyGirin
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Peptides

  • D-Pyroglutamic acid
  • alpha-methyl-L-phenylalanine
  • 3-phenyllactic acid
  • 2-hydroxyacetic acid
  • (2S)-6-amino-2-hydroxyhexanoic acid
Symbol Name Structure Leaving group (attachment atom-leaving group atom)
D-Pyr D-Pyroglutamic acid D-Pyroglutamic acid.zip R1=H (0-9), R2=OH (6-8)
aMePhe alpha-methyl-L-phenylalanine Alpha-methyl-L-phenylalanine.zip R1=H (0-5), R2=OH (2-3)
PhLA 3-phenyllactic acid 3-phenyllactic acid.zip R2=OH (8-9)
DAGlyO 2-hydroxyacetic acid 2-hydroxyacetic acid.zip R1=H (4-5), R2=OH (1-2)
DALys (2S)-6-amino-2-hydroxyhexanoic acid (old name: 6-amino-2-hydroxyhexanoic acid) 6-amino-2-hydroxyhexanoic acid.zip R1=H (0-11), R2=OH (2-3), R3=H (9-10)

Nucleotides

  • 5-Nitroindole
  • 5-Bromo-deoxyuridine
  • 5-hydroxybutynl-2’-deoxyuridine
  • Amino Modifier C6 dT
  • 8-aza-7-deazaguanosine
  • Hydroxymethyl dC
  • 2,6-Diaminopurine
Symbol Name Structure Leaving group (attachment atom-leaving group atom)
5NitInd 5-Nitroindole 5-Nitroindole.zip R1=H (18-19), R2=OH (21-22)
5-Bromo dU (new symbol: 5Br-dU) 5-Bromo-deoxyuridine 5-Bromo-deoxyridine.zip R1=H (7-8), R2=OH (10-11)
Super T 5-hydroxybutynl-2’-deoxyuridine 5-hydroxybutynl-2-deoxyuridine.zip R1=H (7-8), R2=OH (10-11)
AmMC6T Amino Modifier C6 dT Amino Modifier C6 dT.zip R1=H (7-8), R2=OH (10-11), R3=H (32-34), R4=H (32-33)
Super G 8-aza-7-deazaguanosine 8-aza-7-deazaguanosine.zip R1=H (7-8), R2=OH (10-11)
5HydMe-dC (new symbol: 5hMedC) Hydroxymethyl dC Hydroxymethyl dC.zip R1=H (6-7), R2=OH (9-10)
2-Amino-dA (new symbol: 2-damdA) 2,6-Diaminopurine 2,6-Diaminopurine.zip R1=H (6-7), R2=OH (9-10)

Phosphates

  • Phosphorodiamidate
  • Phosporothioate
Symbol Name Structure Leaving group (attachment atom-leaving group atom)
m2np Phosphorodiamidate Phosphorodiamidate.zip R1=OH (0-1), R2=NH2 (0-2)
sP Phosporothioate Phosphothioate.zip R1=OH (1-0), R2=OH (1-4)

Bases

  • 3-Methyluracil
  • N7-methylguanine
Symbol Name Structure Leaving group (attachment atom-leaving group atom)
m3U 3-Methyluracil 3-Methyluracil.zip R1=H (3-6)
m7G N7-methylguanine (old name: 7-Methylguanine) N7-methylguanine.zip R1=H (6-12)

Sugars

  • 5-(R)-Methyl-(R)-cEt BNA
  • 5-(R)-Methyl-(S)-cEt BNA
  • 5-(S)-Methyl-(R)-cEt BNA
  • 5-(S)-Methyl-(S)-cEt BNA
Symbol Name Structure Leaving group (attachment atom-leaving group atom)
5R6Rm5 5-(R)-Methyl-(R)-cEt BNA 5-(R)-Methyl-(R)-cEt BNA.zip R1=H (6-8), R2=H (10-11), R3=OH (1-9)
5R6Sm5 5-(R)-Methyl-(S)-cEt BNA 5-(R)-Methyl-(S)-cEt BNA.zip R1=H (6-8), R2=H (10-11), R3=OH (1-9)
5S6Rm5 5-(S)-Methyl-(R)-cEt BNA 5-(S)-Methyl-(R)-cEt BNA.zip R1=H (6-8), R2=H (10-11), R3=OH (1-9)
5S6Sm5 5-(S)-Methyl-(S)-cEt BNA 5-(S)-Methyl-(S)-cEt BNA.zip R1=H (6-8), R2=H (10-11), R3=OH (1-9)
@ljubica-milovic ljubica-milovic self-assigned this Aug 20, 2024
@ljubica-milovic ljubica-milovic changed the title Incorrect atoms for R2 of unsplit nucleotides Change structure of monomers Aug 20, 2024
rrodionov91 added a commit that referenced this issue Oct 1, 2024
@rrodionov91
#5325 - Change natural analogue of monomers
02ab839 
#5324 - Change symbols of monomers

#5323 - Change names of monomers

#5195 - Some content problems in monomer library

#5111 - Change structure of monomers
@rrodionov91 rrodionov91 mentioned this issue Oct 1, 2024
Merged
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@rrodionov91 rrodionov91 linked a pull request Oct 1, 2024 that will close this issue
#5325 - Change natural analogue of monomers #5619
Merged
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rrodionov91 added a commit that referenced this issue Oct 3, 2024
@rrodionov91 @AlexeyGirin
#5325 - Change natural analogue of monomers (#5619)
8454ce7 
#5325 - Change natural analogue of monomers
#5324 - Change symbols of monomers
#5323 - Change names of monomers
#5195 - Some content problems in monomer library
#5111 - Change structure of monomers

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>
@AlexeyGirin
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Verified.

  • Ketcher Version 2.26.0-rc.1 Build at 2024-10-04; 18:45:04
  • Indigo Toolkit Version 1.25.0-rc.1.0-g704673fcb-wasm32-wasm-clang-19.0.0
  • Chrome Version 129.0.6668.90 (Official Build) (64-bit)
  • Win10

Guch1g0v pushed a commit that referenced this issue Oct 17, 2024
@rrodionov91 @AlexeyGirin @Guch1g0v
#5325 - Change natural analogue of monomers (#5619)
907ad01 
#5325 - Change natural analogue of monomers
#5324 - Change symbols of monomers
#5323 - Change names of monomers
#5195 - Some content problems in monomer library
#5111 - Change structure of monomers

---------

Co-authored-by: Alexey Girin <agirin@mail.ru>
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#5325 - Change natural analogue of monomers epam/ketcher
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