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 KB_HAT_154

PDB9IFF↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising SASA cached

Promising and worth follow-up

Binding strong Geometry high Native strong SASA done

Strain ΔE

15.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.69, Jaccard 0.50

Burial

77%

Hydrophobic fit

81%

Reason: no major geometry red flags detected

2 protein-contact clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.402

ADMET + ECO + DL

ADMETscore (GDS)

0.416

absorption · distr. · metab.

DLscore

0.448

drug-likeness

GDS₂ (2-block)

0.382

ECO + ADMET

P(SAFE)

7.1%

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.951 kcal/mol/HA) ✓ Good fit quality (FQ -8.52) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (15.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-22.826

kcal/mol

-0.951

kcal/mol/HA

Fit Quality

-8.52

FQ (Leeson)

HAC

heavy atoms

337

LogP

3.58

cLogP

Final rank

1.6574

rank score

Inter norm

-1.068

normalised

Contacts

H-bonds 4

Strain ΔE

15.7 kcal/mol

SASA buried

77%

Lipo contact

81% BSA apolar/total

SASA unbound

597 Å²

Apolar buried

372 Å²

Interaction summary

HBD 2 HY 9 PI 0 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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	9	Native recall	0.69
Jaccard	0.50	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
108	1.657387957289586	-1.06825	-22.8259	4	14	9	0.69	-	-	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 -22.826kcal/mol

Ligand efficiency (LE) -0.9511kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.523

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 337.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.58

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.66kcal/mol

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

Docked FF energy 32.12kcal/mol

Minimised FF energy 16.46kcal/mol

SASA & burial

✓ computed

SASA (unbound) 596.6Å²

Total solvent-accessible surface area of free ligand

BSA total 461.6Å²

Buried surface area upon binding

BSA apolar 372.0Å²

Hydrophobic contacts buried

BSA polar 89.6Å²

Polar contacts buried

Fraction buried 77.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 80.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2967.5Å²

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 4005.2Å²

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

Complex non-polar SASA 1521.2Å²

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