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 Z49605089

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

Promising but geometrically suspicious

Binding strong Geometry low Native mixed SASA done

Strain ΔE

42.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.54, Jaccard 0.32

Burial

78%

Hydrophobic fit

75%

Reason: strain 42.3 kcal/mol

strain ΔE 42.3 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 68% of hydrophobic surface is solvent-exposed (13/19 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

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 (-0.793 kcal/mol/HA) ✓ Good fit quality (FQ -7.57) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (42.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-23.004

kcal/mol

-0.793

kcal/mol/HA

Fit Quality

-7.57

FQ (Leeson)

HAC

heavy atoms

419

LogP

0.56

cLogP

Final rank

4.2361

rank score

Inter norm

-0.857

normalised

Contacts

H-bonds 10

Strain ΔE

42.3 kcal/mol

SASA buried

78%

Lipo contact

75% BSA apolar/total

SASA unbound

688 Å²

Apolar buried

400 Å²

Interaction summary

HBD 1 HBA 3 HY 8 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

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

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: strict.

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	7	Native recall	0.54
Jaccard	0.32	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
631	4.236059750523228	-0.857456	-23.0043	10	16	7	0.54	-	-	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 -23.004kcal/mol

Ligand efficiency (LE) -0.7933kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.572

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

Heavy atom count 29HA

Physicochemical properties

Molecular weight 419.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.56

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 42.35kcal/mol

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

Docked FF energy 25.87kcal/mol

Minimised FF energy -16.48kcal/mol

SASA & burial

✓ computed

SASA (unbound) 687.6Å²

Total solvent-accessible surface area of free ligand

BSA total 532.6Å²

Buried surface area upon binding

BSA apolar 399.8Å²

Hydrophobic contacts buried

BSA polar 132.8Å²

Polar contacts buried

Fraction buried 77.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 75.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2985.2Å²

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 1542.7Å²

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