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 OHD_Leishmania_347

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

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

27.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.50, Jaccard 0.27, H-bond role recall 1.00

Burial

79%

Hydrophobic fit

91%

Reason: 21 internal clashes

21 intramolecular clashes 45% of hydrophobic surface appears solvent-exposed (15/33 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.621 kcal/mol/HA) ✓ Good fit quality (FQ -6.41) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ High strain energy (27.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (21)

Score

-23.608

kcal/mol

-0.621

kcal/mol/HA

Fit Quality

-6.41

FQ (Leeson)

HAC

heavy atoms

503

LogP

4.25

cLogP

Final rank

3.4581

rank score

Inter norm

-0.626

normalised

Contacts

H-bonds 3

Strain ΔE

27.1 kcal/mol

SASA buried

79%

Lipo contact

91% BSA apolar/total

SASA unbound

763 Å²

Apolar buried

547 Å²

Interaction summary

HBA 2 HY 7 PI 3 CLASH 0

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

No clash · clashes detected for this pose.

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	6	Native recall	0.50
Jaccard	0.27	RMSD	-
HB strict	1	Strict recall	1.00
HB same residue+role	1	HB role recall	1.00
HB same residue	1	HB residue recall	1.00

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
15	3.4581355020275186	-0.62562	-23.6083	3	16	6	0.50	1.00	-	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 -23.608kcal/mol

Ligand efficiency (LE) -0.6213kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.405

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

Heavy atom count 38HA

Physicochemical properties

Molecular weight 502.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.25

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 27.12kcal/mol

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

Docked FF energy 77.64kcal/mol

Minimised FF energy 50.52kcal/mol

SASA & burial

✓ computed

SASA (unbound) 762.5Å²

Total solvent-accessible surface area of free ligand

BSA total 600.7Å²

Buried surface area upon binding

BSA apolar 547.3Å²

Hydrophobic contacts buried

BSA polar 53.5Å²

Polar contacts buried

Fraction buried 78.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 91.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -6665.8Å²

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 2105.7Å²

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