Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand ulfkktlib_169

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

19.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.87, H-bond role recall 0.56

Burial

65%

Hydrophobic fit

87%

Reason: 6 internal clashes

6 intramolecular clashes 70% of hydrophobic surface is solvent-exposed (16/23 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. 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 ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.723 kcal/mol/HA) ✓ Good fit quality (FQ -6.83) ✓ Good H-bonds (4 bonds) ✓ Good burial (65% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Moderate strain (19.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-20.248

kcal/mol

-0.723

kcal/mol/HA

Fit Quality

-6.83

FQ (Leeson)

HAC

heavy atoms

386

LogP

3.53

cLogP

Final rank

1.9885

rank score

Inter norm

-0.864

normalised

Contacts

H-bonds 8

Strain ΔE

19.2 kcal/mol

SASA buried

65%

Lipo contact

87% BSA apolar/total

SASA unbound

737 Å²

Apolar buried

417 Å²

Interaction summary

HBD 1 HBA 3 HY 3 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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	0.87	RMSD	-
HB strict	4	Strict recall	0.33
HB same residue+role	5	HB role recall	0.56
HB same residue	6	HB residue recall	0.75

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
132	1.9885127352526542	-0.864012	-20.2477	8	14	13	0.93	0.56	-	no	Current
110	4.693817183119807	-0.845324	-22.7912	11	18	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 -20.248kcal/mol

Ligand efficiency (LE) -0.7231kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.827

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 385.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.53

Lipinski: ≤ 5

Rotatable bonds 11

Conformational strain (MMFF94s)

Strain energy (ΔE) 19.16kcal/mol

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

Docked FF energy 65.02kcal/mol

Minimised FF energy 45.86kcal/mol

SASA & burial

✓ computed

SASA (unbound) 737.2Å²

Total solvent-accessible surface area of free ligand

BSA total 477.4Å²

Buried surface area upon binding

BSA apolar 417.4Å²

Hydrophobic contacts buried

BSA polar 60.1Å²

Polar contacts buried

Fraction buried 64.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 87.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2378.5Å²

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 777.4Å²

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