Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T20

T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)

Ligand Z59307967

PDB9IFH↗

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 strong SASA done

Strain ΔE

12.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00

Burial

58%

Hydrophobic fit

88%

Reason: 14 internal clashes

14 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model

ECOscore

0.561

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.440

ADMET + ECO + DL

ADMETscore (GDS)

0.383

absorption · distr. · metab.

DLscore

0.469

drug-likeness

P(SAFE)

0.84

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.698 kcal/mol/HA) ✓ Good fit quality (FQ -6.43) ✓ Good H-bonds (3 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Moderate strain (12.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)

Score

-18.137

kcal/mol

-0.698

kcal/mol/HA

Fit Quality

-6.43

FQ (Leeson)

HAC

heavy atoms

348

LogP

3.08

cLogP

Final rank

4.1432

rank score

Inter norm

-0.747

normalised

Contacts

H-bonds 3

Strain ΔE

12.3 kcal/mol

SASA buried

58%

Lipo contact

88% BSA apolar/total

SASA unbound

607 Å²

Apolar buried

310 Å²

Interaction summary

HBD 1 HBA 2 HY 4 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)

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

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	9IFH	Contacts	8
Pose	Open native pose	HB	0
IFP residues	ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap	6	Native recall	0.75
Jaccard	0.43	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	0	HB residue recall	0.00

Protein summary

492 residues

Protein target	T20	Atoms	7539
Residues	492	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:221

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:FAD501

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
485	4.1431914032475	-0.747044	-18.1367	3	12	6	0.75	0.00	-	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 -18.137kcal/mol

Ligand efficiency (LE) -0.6976kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.427

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 348.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.08

Lipinski: ≤ 5

Rotatable bonds 2

Conformational strain (MMFF94s)

Strain energy (ΔE) 12.31kcal/mol

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

Docked FF energy -25.20kcal/mol

Minimised FF energy -37.51kcal/mol

SASA & burial

✓ computed

SASA (unbound) 606.8Å²

Total solvent-accessible surface area of free ligand

BSA total 354.0Å²

Buried surface area upon binding

BSA apolar 310.5Å²

Hydrophobic contacts buried

BSA polar 43.5Å²

Polar contacts buried

Fraction buried 58.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 87.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3080.6Å²

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 4069.8Å²

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

Complex non-polar SASA 1509.6Å²

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