Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T17

T. brucei TR (Doorstop site) T. brucei Doorstop site

Ligand OSA_Lib_20

PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry high Native strong SASA done

Strain ΔE

26.4 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.92, Jaccard 0.50, H-bond role recall 0.00

Burial

83%

Hydrophobic fit

97%

Reason: no major geometry red flags detected

1 protein-contact clashes 47% of hydrophobic surface appears solvent-exposed (14/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.662 kcal/mol/HA) ✓ Good fit quality (FQ -6.68) ✓ Good H-bonds (3 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (97%) ✗ High strain energy (26.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-23.180

kcal/mol

-0.662

kcal/mol/HA

Fit Quality

-6.68

FQ (Leeson)

HAC

heavy atoms

477

LogP

0.96

cLogP

Final rank

3.0347

rank score

Inter norm

-0.658

normalised

Contacts

H-bonds 3

Strain ΔE

26.4 kcal/mol

SASA buried

83%

Lipo contact

97% BSA apolar/total

SASA unbound

800 Å²

Apolar buried

638 Å²

Interaction summary

HBD 2 HBA 1 HY 8 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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	5S9T	Contacts	12
Pose	Open native pose	HB	0
IFP residues	ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap	11	Native recall	0.92
Jaccard	0.50	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	0	HB residue recall	0.00

Protein summary

1033 residues

Protein target	T17	Atoms	15160
Residues	1033	Chains	2
Residue summary	VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0

Kept cofactors / ions

A:FAD501 B: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
157	3.034738630922546	-0.658498	-23.1802	3	21	11	0.92	0.00	-	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 -23.180kcal/mol

Ligand efficiency (LE) -0.6623kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.680

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

Heavy atom count 35HA

Physicochemical properties

Molecular weight 476.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.96

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 26.39kcal/mol

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

Docked FF energy 173.71kcal/mol

Minimised FF energy 147.31kcal/mol

SASA & burial

✓ computed

SASA (unbound) 800.1Å²

Total solvent-accessible surface area of free ligand

BSA total 660.9Å²

Buried surface area upon binding

BSA apolar 638.3Å²

Hydrophobic contacts buried

BSA polar 22.6Å²

Polar contacts buried

Fraction buried 82.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 96.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -6783.5Å²

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 8063.1Å²

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

Complex non-polar SASA 2048.4Å²

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