Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand Z56808872

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 medium Native strong SASA done

Strain ΔE

11.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.72, H-bond role recall 0.44

Burial

83%

Hydrophobic fit

71%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

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 (-0.964 kcal/mol/HA) ✓ Good fit quality (FQ -8.88) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Moderate strain (11.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Internal clashes (7)

Score

-25.056

kcal/mol

-0.964

kcal/mol/HA

Fit Quality

-8.88

FQ (Leeson)

HAC

heavy atoms

342

LogP

3.42

cLogP

Final rank

1.1695

rank score

Inter norm

-1.004

normalised

Contacts

H-bonds 12

Strain ΔE

11.7 kcal/mol

SASA buried

83%

Lipo contact

71% BSA apolar/total

SASA unbound

579 Å²

Apolar buried

340 Å²

Interaction summary

HBD 1 HBA 6 HY 3 PI 2 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

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	0.72	RMSD	-
HB strict	6	Strict recall	0.50
HB same residue+role	4	HB role recall	0.44
HB same residue	4	HB residue recall	0.50

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
670	1.1694668289267791	-1.00387	-25.0558	12	17	13	0.93	0.44	-	no	Current
660	2.851733675615678	-0.731489	-18.3231	4	11	0	0.00	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 -25.056kcal/mol

Ligand efficiency (LE) -0.9637kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.879

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 342.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.42

Lipinski: ≤ 5

Rotatable bonds 2

Conformational strain (MMFF94s)

Strain energy (ΔE) 11.73kcal/mol

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

Docked FF energy 65.99kcal/mol

Minimised FF energy 54.26kcal/mol

SASA & burial

✓ computed

SASA (unbound) 579.0Å²

Total solvent-accessible surface area of free ligand

BSA total 478.1Å²

Buried surface area upon binding

BSA apolar 340.1Å²

Hydrophobic contacts buried

BSA polar 137.9Å²

Polar contacts buried

Fraction buried 82.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 71.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2151.4Å²

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 729.7Å²

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