Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand TC164

PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry high Native strong SASA done

Strain ΔE

19.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

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

Burial

67%

Hydrophobic fit

89%

Reason: no major geometry red flags detected

1 protein-contact clashes 61% of hydrophobic surface is solvent-exposed (19/31 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

vB — Very bioaccumulative (BCF>5000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.924 kcal/mol/HA) ✓ Good fit quality (FQ -9.17) ✓ Good H-bonds (3 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (19.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)

Score

-30.495

kcal/mol

-0.924

kcal/mol/HA

Fit Quality

-9.17

FQ (Leeson)

HAC

heavy atoms

445

LogP

6.47

cLogP

Final rank

1.9038

rank score

Inter norm

-0.873

normalised

Contacts

H-bonds 5

Strain ΔE

19.0 kcal/mol

SASA buried

67%

Lipo contact

89% BSA apolar/total

SASA unbound

758 Å²

Apolar buried

451 Å²

Interaction summary

HBD 1 HBA 2 HY 3 PI 0 CLASH 1

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	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
198	1.9038326798593825	-0.873097	-30.4949	5	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 -30.495kcal/mol

Ligand efficiency (LE) -0.9241kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.169

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 444.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 6.47

Lipinski: ≤ 5

Rotatable bonds 2

Conformational strain (MMFF94s)

Strain energy (ΔE) 19.01kcal/mol

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

Docked FF energy 95.04kcal/mol

Minimised FF energy 76.03kcal/mol

SASA & burial

✓ computed

SASA (unbound) 757.9Å²

Total solvent-accessible surface area of free ligand

BSA total 505.9Å²

Buried surface area upon binding

BSA apolar 450.6Å²

Hydrophobic contacts buried

BSA polar 55.4Å²

Polar contacts buried

Fraction buried 66.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 89.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2396.4Å²

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 771.6Å²

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