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 TC483

PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

37.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.67, Jaccard 0.38, H-bond role recall 1.00

Burial

72%

Hydrophobic fit

80%

Reason: 15 internal clashes

5 protein-contact clashes 15 intramolecular clashes

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 Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.535 kcal/mol/HA) ✓ Good fit quality (FQ -5.62) ✓ Good H-bonds (4 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (37.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (15)

Score

-21.945

kcal/mol

-0.535

kcal/mol/HA

Fit Quality

-5.62

FQ (Leeson)

HAC

heavy atoms

560

LogP

3.95

cLogP

Final rank

1.9753

rank score

Inter norm

-0.569

normalised

Contacts

H-bonds 6

Strain ΔE

37.2 kcal/mol

SASA buried

72%

Lipo contact

80% BSA apolar/total

SASA unbound

848 Å²

Apolar buried

485 Å²

Interaction summary

HBD 1 HBA 3 HY 8 PI 1 CLASH 0

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

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	8	Native recall	0.67
Jaccard	0.38	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
260	1.7896829464386903	-0.560892	-25.23	3	16	0	0.00	0.00	-	no	Open
268	1.9752581535034928	-0.56884	-21.9448	6	17	8	0.67	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 -21.945kcal/mol

Ligand efficiency (LE) -0.5352kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.624

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

Heavy atom count 41HA

Physicochemical properties

Molecular weight 559.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.95

Lipinski: ≤ 5

Rotatable bonds 12

Conformational strain (MMFF94s)

Strain energy (ΔE) 37.22kcal/mol

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

Docked FF energy 116.94kcal/mol

Minimised FF energy 79.72kcal/mol

SASA & burial

✓ computed

SASA (unbound) 848.0Å²

Total solvent-accessible surface area of free ligand

BSA total 609.2Å²

Buried surface area upon binding

BSA apolar 485.2Å²

Hydrophobic contacts buried

BSA polar 124.0Å²

Polar contacts buried

Fraction buried 71.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 79.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -6718.1Å²

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 8063.1Å²

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

Complex non-polar SASA 2064.3Å²

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