Zentrum für Bioinformatik: Universität Hamburg

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Ligands
Pockets

Ligands

4SP_A_1298
S(=O)(=O)(N)c1ccc(Nc2nc(OCC3CCCCC3)c4NC=Nc4n2)cc1

4SP_C_1298
S(=O)(=O)(N)c1ccc(Nc2nc(OCC3CCCCC3)c4NC=Nc4n2)cc1

Pockets

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GeoMine Textual, numerical, and chemical 3D searching in the PDB

GeoMine enables textual, numerical, chemical and 3D searching in ligand-bound and ligand-unbound binding sites of the entire PDB dataset ^1,^2,³. The tool is based on the tools Pelikan⁴ and PoseEdit⁵.

^{1. Diedrich, K.; Ehrt, C.; Graef, J.; Poppinga, M.; Ritter, N.; Rarey, M.,
User-centric design of a 3D search interface for protein-ligand complexes.
J Comput Aided Mol Des 2024, 38 (23). DOI:

https://doi.org/10.1007/s10822-024-00563-3}
^{2. Graef, J.; Ehrt, C.; Diedrich, K.; Poppinga, M.; Ritter, N.;
Rarey, M., Searching Geometric Patterns in Protein Binding Sites and
Their Application to Data Mining in Protein Kinase Structures.
J Med Chem 2022, 65 (2), 1384-1395. DOI:

https://doi.org/10.1021/acs.jmedchem.1c01046}
^{3. Diedrich, K.; Graef, J.; Schoning-Stierand, K.; Rarey,
M., GeoMine: interactive pattern mining of protein-ligand interfaces
in the Protein Data Bank. Bioinformatics 2021, 37 (3), 424-425. DOI:

https://doi.org/10.1093/bioinformatics/btaa693}
^{4. Inhester, T.; Bietz, S.; Hilbig, M.; Schmidt, R.;
Rarey, M., Index-Based Searching of Interaction Patterns in Large Collections of
Protein-Ligand Interfaces. J Chem Inf Model 2017, 57 (2), 148-158. DOI:

https://doi.org/10.1021/acs.jcim.6b00561}
^{5. Diedrich, K.; Krause, B.; Berg, O.; Rarey, M., PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J Comput Aided Mol Des 2023, 37, 491-503. DOI:

https://doi.org/10.1007/s10822-023-00522-4}

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PoseEdit

PoseEdit ¹ uses the PoseView algorithm and the InteractionDrawer JavaScript library (https://github.com/rareylab/InteractionDrawer) for the fully automatic drawing of highly interactive 2D ligand interaction diagrams. Structures are depicted according to IUPAC recommendations. Calculated interactions (hydrogen bonds, cation-pi interactions, pi-stackings, ionic interactions, and metal interactions) of the ligand with nucleic acids, amino acids, and metals are depicted as colored dashed lines. Hydrophobic contacts are visualized by labeled green splines. The binding sites and the interactions occurring within were calculated by Protoss, DoGSite3, and GeoMine.

^{1. Diedrich, K.; Krause, B.; Berg, O.; Rarey, M., PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J Comput Aided Mol Des 2023. DOI:

https://doi.org/10.1007/s10822-023-00522-4}

Check the help pages for PoseEdit and its REST API for further information.

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Points

	Point ID	Element	Type	Molecule		ChildRowData		NglID	LigandType	Color

Distances

	Distance ID	Point ID 1	Point ID 2	Length	Tolerance		NglID	Color

Interactions

	Interaction ID	Point ID 1	Point ID 2	Type		NglID	Color

Angles

	Angle ID	Point-Point ID 1	Point-Point ID 2	Size	Tolerance		NglID	Color

Filtertype

Number of PDBs in list:

Component	Test Short Name	Test Description	Configurations
			Astex-like	Iridium-like	Platinum	Combined
Complex	Resolution	Resolution at most 2.5 Å	yes	3.5 - yes	yes	yes
	DPI	Model diffraction precision index (Goto) at most 0.42	no	no	yes	yes
	R factor	Model R Factor at most 0.4	no	yes	yes	yes
	R free factor	Model R Free Factor at most 0.45	no	no	yes	yes
	Overfitting	Difference between R and R Free Factor at most 0.05	no	no	no	yes
	Model significance	Model is significant (Rfree < 0.45 and Resolution < 3.5 Å)	no	no	no	yes
	Deposition date	PDB deposition date later than 11-AUG-00	yes	no	no	no
ActiveSite	RSCC	RSCC at least 0.7	no	no (yes)	no	no
ActiveSite	EDIA_m per residue	Percentage of all residues with EDIA_m below 0.7 (tolerated: up to 0%)	yes (no)	yes (no)	no	yes
ActiveSite	B factor ratio	Absolute active site to ligand B factor ratio at least 0.5	no	no	no	yes
ActiveSite	Occupancy	Percentage of atoms with occupancy of at least 1 (tolerated: up to 0%)	no	yes	no	yes
ActiveSite	Intramolecular clash score	Intramolecular clash for no heavy atom pair (sum vdw - 0.9Å)	no	no	no	yes
		Intramolecular clash for no heavy atom pair (0.8*(sum vdw))	no	no	no	no
ActiveSite	Intermolecular clash score	Intermolecular clash for no heavy atom pair (sum vdw - 0.9Å)	yes	no	no	yes
		Intermolecular clash for no heavy atom pair (0.8*(sum vdw))	no	no	no	no
ActiveSite	VSEPR bond angles	Percentage of bond angles differing by more than 16 ° (tolerated: up to 0%)	no	no	no	yes
ActiveSite	Unusual bond lengths	Percentage of bond lengths differing by more than 0.2 Å (tolerated: up to 0%)	no	no	no	yes
Ligand	Number of heavy atoms	At least 10 heavy atoms present	yes	no	yes	yes
Ligand	Maximum atomic B factor	Atomic B Factor is maximally 50 Å² for 100% of atoms	no	no	no	yes
Ligand	VSEPR bond angles	Percentage of bond angles differing by more than 16 ° (tolerated: up to 0%)	no	no	yes	yes
Ligand	Unusual bond lengths	Percentage of bond lengths differing by more than 0.2 Å (tolerated: up to 0%)	no	no	yes	yes
Ligand	Torsion angles	Number of torsions beyond the second TorLib tolerance interval	no	no	no	yes
Ligand	Crystal symmetry contacts	At most 0 crystal symmetry contacts closer than 6 Å to the ligand	yes	yes	no	yes
Ligand	EDIA_m	EDIA_m score at least 0.8	yes	no	yes	yes
		EDIA_i score at least 0.8	no	yes	no	no
Ligand	Intramolecular clash score	Intramolecular clash for no heavy atom pair (sum vdw - 0.9Å)	yes	no	yes	yes
		Intramolecular clash for no heavy atom pair (0.8*(sum vdw))	no	no	no	no
Ligand	LogP	LogP is at most 5	yes	no	no	yes
Ligand	Molecular weight	Molecular weight is at least 100 and at most 600u	yes	no	130 - 600u - yes	yes
Ligand	Lipinski acceptors	At most 10 Lipinski acceptors	yes	no	no	yes
Ligand	Lipinski donors	At most 5 Lipinski donors	yes	no	no	yes
Ligand	Number of peptides	At most 3 peptides are present	yes	no	no	yes
Ligand	Number of rotatable bonds	Number of rotatable bonds are at most 16	10 - yes	no	yes	yes
Ligand	Number of stereo centers	At most 5 stereo centers present	no	no	no	yes
Ligand	Occupancy	Percentage of atoms with occupancy of at least 1 (tolerated: up to 0%)	no	yes	yes	yes
Ligand	OWAB	OWAB is at most 50 Å²	no	no	no	yes
Ligand	RSCC	RSCC is at least 0.7	no	no	no	no
Ligand	SMARTS	Ligand matches none of the SMARTS in exclusion and if defined at least one in the inclusion SMARTS list	yes	no	yes	yes
Ligand	HET code	HET code does not match the exclusion list	yes	no	yes	yes

ZBH - Center for Bioinformatics