Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Change structure of monomers #5111

Closed
20 tasks done
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
Assignees
@ljubica-milovic
Labels
Monomer Library
Milestone
Ketcher 2.26.0-rc.1

Comments

@ljubica-milovic
Copy link
Collaborator

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

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
9 tasks
@rrodionov91 rrodionov91 linked a pull request Oct 1, 2024 that will close this issue
#5325 - Change natural analogue of monomers #5619
Merged
9 tasks
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 <[email protected]>
@AlexeyGirin
Copy link
Collaborator

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 <[email protected]>
This was referenced Feb 24, 2025
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ljubica-milovic ljubica-milovic

Labels
Monomer Library
Projects
None yet
Milestone
Ketcher 2.26.0-rc.1
Development

Successfully merging a pull request may close this issue.

#5325 - Change natural analogue of monomers epam/ketcher
2 participants
@AlexeyGirin @ljubica-milovic