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_chagas_97

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

13.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.62, Jaccard 0.38

Burial

75%

Hydrophobic fit

69%

Reason: no major geometry red flags detected

2 protein-contact clashes 43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.698

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.460

ADMET + ECO + DL

ADMETscore (GDS)

0.403

absorption · distr. · metab.

DLscore

0.418

drug-likeness

P(SAFE)

0.12

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.881 kcal/mol/HA) ✓ Good fit quality (FQ -8.32) ✓ Good H-bonds (5 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Moderate strain (13.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-24.665

kcal/mol

-0.881

kcal/mol/HA

Fit Quality

-8.32

FQ (Leeson)

HAC

heavy atoms

411

LogP

4.11

cLogP

Final rank

3.1616

rank score

Inter norm

-0.916

normalised

Contacts

H-bonds 6

Strain ΔE

13.7 kcal/mol

SASA buried

75%

Lipo contact

69% BSA apolar/total

SASA unbound

658 Å²

Apolar buried

338 Å²

Interaction summary

HBD 2 HBA 3 HY 6 PI 0 CLASH 2

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	8	Native recall	0.62
Jaccard	0.38	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
145	2.3944530643812723	-0.832618	-22.5355	6	19	0	0.00	-	-	no	Open
140	3.161585895070036	-0.916178	-24.6646	6	16	8	0.62	-	-	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 -24.665kcal/mol

Ligand efficiency (LE) -0.8809kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.316

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 410.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.11

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 13.67kcal/mol

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

Docked FF energy 29.95kcal/mol

Minimised FF energy 16.28kcal/mol

SASA & burial

✓ computed

SASA (unbound) 657.9Å²

Total solvent-accessible surface area of free ligand

BSA total 492.6Å²

Buried surface area upon binding

BSA apolar 338.4Å²

Hydrophobic contacts buried

BSA polar 154.2Å²

Polar contacts buried

Fraction buried 74.9%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 68.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2939.2Å²

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 1546.1Å²

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