Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T18

T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)

Ligand OHD_TB2020_2

PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Likely artefact or unreliable pose

Binding strong Geometry medium Native strong SASA done

Strain ΔE

41.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.69, Jaccard 0.56

Burial

51%

Hydrophobic fit

92%

Reason: no major geometry red flags detected

4 protein-contact clashes 4 intramolecular clashes 64% of hydrophobic surface is solvent-exposed (21/33 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.406 kcal/mol/HA) ✓ Good fit quality (FQ -4.41) ✓ Good burial (51% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ Extreme strain energy (41.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (15)

Score

-19.103

kcal/mol

-0.406

kcal/mol/HA

Fit Quality

-4.41

FQ (Leeson)

HAC

heavy atoms

652

LogP

3.51

cLogP

Final rank

2.3065

rank score

Inter norm

-0.445

normalised

Contacts

H-bonds 2

Strain ΔE

41.2 kcal/mol

SASA buried

51%

Lipo contact

92% BSA apolar/total

SASA unbound

964 Å²

Apolar buried

447 Å²

Interaction summary

HBD 2 HY 4 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	6RB5	Contacts	13
Pose	Open native pose	HB	0
IFP residues	ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap	9	Native recall	0.69
Jaccard	0.56	RMSD	-
HB strict	0	Strict recall	-
HB same residue+role	0	HB role recall	-
HB same residue	0	HB residue recall	-

Protein summary

493 residues

Protein target	T18	Atoms	7550
Residues	493	Chains	1
Residue summary	VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:FAD501

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
46	2.3065480461668835	-0.44477	-19.1028	2	12	9	0.69	-	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -19.103kcal/mol

Ligand efficiency (LE) -0.4064kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.408

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 47HA

Physicochemical properties

Molecular weight 651.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.51

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 41.22kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 221.51kcal/mol

Minimised FF energy 180.29kcal/mol

SASA & burial

✓ computed

SASA (unbound) 964.0Å²

Total solvent-accessible surface area of free ligand

BSA total 488.1Å²

Buried surface area upon binding

BSA apolar 447.0Å²

Hydrophobic contacts buried

BSA polar 41.1Å²

Polar contacts buried

Fraction buried 50.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 91.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3379.1Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 4076.6Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 1565.3Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)