Compound data, library construction schemes and preparation routine for small drug-like molecules as ligands in docking and for further analysis.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
Snapshots: No snapshots
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Assays: Rigid-body docking studies
Summary of fragments that were used to construct an in silico pteridine library with corresponding fragment identifiers. Connections between the fragments are shown outside the colored boxes. Compounds were composed of a core fragment (C1-C3), an N10 fragment (N1-N7), a PABA fragment (P1-P10) and, for any PABA fragment except P8, P9 and P10, a tail fragment (T1E1-T7).
Zip archive of N1 protonated reference and newly synthesized pteridines (series 1-5) in SDF format.
Compound SMILES of resynthesized or newly designed pteridine compounds 1b, 1c, 2a-e, 3a-e, 4a-j and 5a-f used for ligand preparation within Maestro (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Maestro.). SMILES strings and compound identifiers are comma-separated and can be readily imported in Maestro.
This SOP describes the preparation of pteridine ligand 3D structures from SMILES or other input formats with the LigPrep routine as embedded in Schrödinger Maestro for usage in docking runs and in silico ADME-Tox property prediction.