Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand TC48

PDB3K7O↗

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 but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

14.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.81, H-bond role recall 0.33

Burial

77%

Hydrophobic fit

94%

Reason: 6 internal clashes

6 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (11/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.052 kcal/mol/HA) ✓ Good fit quality (FQ -9.57) ✓ Good H-bonds (3 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (94%) ✗ Moderate strain (14.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-26.310

kcal/mol

-1.052

kcal/mol/HA

Fit Quality

-9.57

FQ (Leeson)

HAC

heavy atoms

343

LogP

4.57

cLogP

Final rank

1.9483

rank score

Inter norm

-0.977

normalised

Contacts

H-bonds 4

Strain ΔE

14.2 kcal/mol

SASA buried

77%

Lipo contact

94% BSA apolar/total

SASA unbound

598 Å²

Apolar buried

433 Å²

Interaction summary

HBD 1 HBA 2 HY 3 PI 0 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

No pi · π–π interactions detected for this pose.

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	3K7O	Contacts	14
Pose	Open native pose	HB	0
IFP residues	ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap	13	Native recall	0.93
Jaccard	0.81	RMSD	-
HB strict	3	Strict recall	0.25
HB same residue+role	3	HB role recall	0.33
HB same residue	3	HB residue recall	0.38

Protein summary

305 residues

Protein target	T21	Atoms	4646
Residues	305	Chains	2
Residue summary	ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
180	1.948262421663869	-0.977428	-26.3104	4	15	13	0.93	0.33	-	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 -26.310kcal/mol

Ligand efficiency (LE) -1.0524kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.567

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 342.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.57

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 14.18kcal/mol

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

Docked FF energy 70.31kcal/mol

Minimised FF energy 56.13kcal/mol

SASA & burial

✓ computed

SASA (unbound) 597.5Å²

Total solvent-accessible surface area of free ligand

BSA total 460.4Å²

Buried surface area upon binding

BSA apolar 433.1Å²

Hydrophobic contacts buried

BSA polar 27.3Å²

Polar contacts buried

Fraction buried 77.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 94.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2298.2Å²

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 2482.0Å²

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

Complex non-polar SASA 751.8Å²

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