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 ulfkktlib_2301

PDB9IFF↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native mixed SASA done

Strain ΔE

21.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.54, Jaccard 0.32

Burial

82%

Hydrophobic fit

85%

Reason: 8 internal clashes

8 intramolecular clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.415

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.425

ADMET + ECO + DL

ADMETscore (GDS)

0.442

absorption · distr. · metab.

DLscore

0.402

drug-likeness

P(SAFE)

0.18

GDS classification

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.096 kcal/mol/HA) ✓ Good fit quality (FQ -9.35) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ High strain energy (21.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-23.020

kcal/mol

-1.096

kcal/mol/HA

Fit Quality

-9.35

FQ (Leeson)

HAC

heavy atoms

282

LogP

1.52

cLogP

Final rank

2.2855

rank score

Inter norm

-1.109

normalised

Contacts

H-bonds 6

Strain ΔE

21.3 kcal/mol

SASA buried

82%

Lipo contact

85% BSA apolar/total

SASA unbound

537 Å²

Apolar buried

378 Å²

Interaction summary

HBD 3 HBA 1 HY 8 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)

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

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	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
332	2.2854664618259806	-1.10903	-23.0201	6	16	7	0.54	-	-	no	Current
201	2.898536666440047	-1.07988	-16.3252	6	17	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 -23.020kcal/mol

Ligand efficiency (LE) -1.0962kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.350

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 282.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.52

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 21.31kcal/mol

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

Docked FF energy 135.68kcal/mol

Minimised FF energy 114.37kcal/mol

SASA & burial

✓ computed

SASA (unbound) 537.2Å²

Total solvent-accessible surface area of free ligand

BSA total 443.0Å²

Buried surface area upon binding

BSA apolar 377.7Å²

Hydrophobic contacts buried

BSA polar 65.3Å²

Polar contacts buried

Fraction buried 82.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 85.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2937.8Å²

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 1528.2Å²

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