Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T15

T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site

Ligand OSA_Lib_228

PDB9IFF↗

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

30.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.77, Jaccard 0.48

Burial

77%

Hydrophobic fit

100%

Reason: no major geometry red flags detected

5 protein-contact clashes 5 intramolecular clashes 37% of hydrophobic surface appears solvent-exposed (11/30 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 ↗

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

✓ Excellent LE (-0.633 kcal/mol/HA) ✓ Good fit quality (FQ -6.34) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (100%) ✗ Very high strain energy (30.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (11)

Score

-21.530

kcal/mol

-0.633

kcal/mol/HA

Fit Quality

-6.34

FQ (Leeson)

HAC

heavy atoms

464

LogP

0.11

cLogP

Final rank

1.4711

rank score

Inter norm

-0.726

normalised

Contacts

H-bonds 2

Strain ΔE

30.0 kcal/mol

SASA buried

77%

Lipo contact

100% BSA apolar/total

SASA unbound

807 Å²

Apolar buried

616 Å²

Interaction summary

HBD 1 HY 9 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.

PI · π–π interactions

No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

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

Name	9IFF	Contacts	13
Pose	Open native pose	HB	0
IFP residues	ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap	10	Native recall	0.77
Jaccard	0.48	RMSD	-
HB strict	0	Strict recall	-
HB same residue+role	0	HB role recall	-
HB same residue	0	HB residue recall	-

Protein summary

489 residues

Protein target	T15	Atoms	7420
Residues	489	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:264; MET:204

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
249	1.4711336958947572	-0.72627	-21.53	2	18	10	0.77	-	-	no	Current
246	3.1345447367687087	-0.700144	-21.7794	2	15	0	0.00	-	-	no	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -21.530kcal/mol

Ligand efficiency (LE) -0.6332kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.336

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

Heavy atom count 34HA

Physicochemical properties

Molecular weight 463.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.11

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 30.05kcal/mol

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

Docked FF energy 323.79kcal/mol

Minimised FF energy 293.75kcal/mol

SASA & burial

✓ computed

SASA (unbound) 806.8Å²

Total solvent-accessible surface area of free ligand

BSA total 618.4Å²

Buried surface area upon binding

BSA apolar 615.8Å²

Hydrophobic contacts buried

BSA polar 2.6Å²

Polar contacts buried

Fraction buried 76.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 99.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3277.9Å²

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 4005.2Å²

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

Complex non-polar SASA 1531.5Å²

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