Sharing a ligand name should only be limited to having the same compound, i.e.
same 2D structure or connectivity. Each deposition should have its own 3D
coordinates. If a different publication gets your ligand 3D coordinates ("2Y59
actually embodies the atomic coordinates from the 2Y2I"), that looks to me an
oversight by PDB. It is hard to believe that PDB intended to use the 3D
coordinates from one entry for the other, ligand or not. In fact, the
restraints as described by the ligand dictionary should also be kept separate
as that reflects how the authors refine their ligand.
Yong
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn
Symmons
Sent: Friday, June 19, 2015 8:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)
By oversimplifying the situation here the PDB does not answer my related point
about competing crystallographers:
My scenario:
Group A deposits structure with new drug - gets their three-letter code for
example ZA3 they then get to check the coordinates and chemical definition of
this ligand.
But suppose a little after that a competing group B deposits their structure
with the same drug which they think is novel - but no...
they get assigned the now described ZA3 which has been checked by the other
group.
Then it is a race to see who gets to publish and release first. And if it is
the second group B who wins then they are publishing the work of their A
competitors - who have done the depositing and checking of the ligand
description.
Sounds unlikely? Well, it actually happened in 2011 for my exact example ZA3 -
present in 2Y2I and in 2Y59 from competing groups.
From the dates in the mmcif it was 2Y2I depositors who set up and had a chance
to review the description of ZA3 ligand. Only to see it released a week before
their crystal structure, when their ZA3 appeared to accompany competing 2Y59!
It is amazing that the PDB did not spot this and arrange a suitable workaround.
Just to check:
mmcif for ZA3 shows it was created for 2Y2I:
...
_chem_comp.pdbx_model_coordinates_db_code 2Y2I
...
But it was modified for release:
...
_chem_comp.pdbx_modified_date 2011-07-22
...
corresponding to the early 2011-07-27 release date of the competing
structure: 2Y59 even though this PDB was _deposited_ second.
The ZA3 ligand definition released with 2Y59 actually embodies the atomic
coordinates from the 2Y2I structure:
<mmcif>
ZA3 O6 O6 O 0 1 N N N 8.279 7.165 40.963 0.311 -1.061 -0.920
O6 ZA3 1
ZA3 C5 C5 C 0 1 N N N 9.132 8.047 40.908 0.147 -0.205 -0.073
C5 ZA3 2 ...
<PDB 2Y2I>
HETATM 3598 O6 ZA3 A1000 8.279 7.165 40.963 1.00 41.25 O
HETATM 3599 C5 ZA3 A1000 9.132 8.047 40.908 1.00 63.20
C ...
Surely a better approach would be to allow both groups a chance to work through
and sign off on independent ligand descriptions?
Then whoever releases first would release both a novel structure and the ligand
definition _they_ deposited and checked. Their priority can then be asserted
and the other group contacted to ask if they agree to accept this definition.
This also has the advantage of better confidentiality pre-publication.
Another problem from any cross-linking of definitions is that say group A are
motivated by reviewers' reports to change the definition of ZA3 pre-release.
Well now the change impinges on the chemical meaning of other group B's
deposited structure. For example ZA3 mmcif has a statement:
ZA3 "Modify aromatic_flag" 2011-06-04 RCSB
so this change was pre-release - but we cannot be sure what motivated this -
whether it was signed off by the 2Y2I authors or the 2Y59 authors (or both?)....
With the accelerating pace of drug discovery for sure this sort of uncertainty
is going to happen again.Unless the PDB have changed their practice for ligand
deposition?
All the best
Martyn
Cambridge.
On Fri, Jun 19, 2015 at 1:49 PM, Sheriff, Steven <steven.sher...@bms.com> wrote:
> All:
>
>
>
> Since the original query was cross-posted on both the COOT mailing
> list and the CCP4BB Rachel Green gave me permission to forward this to
> both. She provides links about the mechanism of assignment of 3-letter
> codes. In the third link below, my original suggestion to the COOT
> mailing list that one could just use UNK is incorrect as that is reserved for
> unknown amino acids.
> According to this document, I should have suggested UNL for an unknown
> ligand.
>
>
>
> Steven
>
>
>
> From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu]
> Sent: Tuesday, June 16, 2015 10:21 AM
> To: Sheriff, Steven
> Cc: info
> Subject: Re: New ligand 3-letter code (help-7071)
>
>
>
> Dear Steven,
>
> During annotation of ligands, all chemical components present in the
> structure are compared against the definitions in the Chemical
> Component Dictionary (http://www.wwpdb.org/data/ccd). If the ligand is
> not in the dictionary, a three letter code is assigned. See
> http://www.wwpdb.org/documentation/policy#toc_assignment. In the
> future, a group of three-letter codes may be set aside to be used
> during refinement to flag new ligands.
>
> Clarification about the ligand ids assignment and in particular the
> usage of UNX/UNL/UNK residues can be found at
> http://www.wwpdb.org/documentation/procedure#toc_2.
>
> Best wishes,
> Rachel
>
>
>
> ________________________________
>
> Rachel Kramer Green, Ph.D.
>
> RCSB PDB
>
> kra...@rcsb.rutgers.edu
>
>
>
> New! Deposit X-ray data with the wwPDB at:
>
> http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon).
>
> ___________________________________________________________
>
> Twitter: https://twitter.com/#!/buildmodels
>
> Facebook: http://www.facebook.com/RCSBPDB
>
>
>
>
>
>
>
> On 6/5/2015 7:50 AM, Sheriff, Steven wrote:
>
> All:
>
>
>
> Why the concern for unassigned three-letter codes? The wwPDB isn’t
> going to let you assign a three-letter code, it will choose its own code.
>
>
>
> At BMS (a pharmaceutical company), we do many hundreds of structures a
> year with ligands and we assign the same, already assigned,
> three-letter code for all of our ligands (unless we have two or more
> different ligands in a single structure, in which case we use two or
> more different already assigned three-letter codes). COOT can mostly handle
> this.
>
>
>
> However, I believe that if you want an unassigned code, the wwPDB has
> set aside UNK[nown] for this purpose.
>
>
>
> Steven
>
>
>
> From: Mailing list for users of COOT Crystallographic Software
> [mailto:c...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson
> Sent: Friday, June 05, 2015 6:28 AM
> To: c...@jiscmail.ac.uk
> Subject: Re: New ligand 3-letter code
>
>
>
> I use your method - trial & error..
>
> It would be nice if at least there was a list somewhere of unassigned codes!
>
>
>
> On 5 June 2015 at 09:16, Lau Sze Yi (SIgN)
> <lau_sze...@immunol.a-star.edu.sg> wrote:
>
> Hi,
>
>
>
> What is the proper way of generating 3-letter code for a new ligand?
> As of now, I insert my ligand in Coot using smiles string and for the
> 3-letter code I picked a non-existent code by trial and error (not
> very efficient). A cif file with corresponding name which I generated
> using Phenix was imported into Coot.
>
>
>
> I am sure there is a proper way of doing this. Appreciate your feedback.
>
>
>
> Regards,
>
> Sze Yi
>
>
>
> ________________________________
>
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>
>
>
> ________________________________
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