Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand KB_HAT_65

PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

47.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.72, H-bond role recall 0.56

Burial

82%

Hydrophobic fit

65%

Reason: strain 47.7 kcal/mol

strain ΔE 47.7 kcal/mol 1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.948 kcal/mol/HA) ✓ Good fit quality (FQ -8.85) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Extreme strain energy (47.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)

Score

-25.602

kcal/mol

-0.948

kcal/mol/HA

Fit Quality

-8.85

FQ (Leeson)

HAC

heavy atoms

369

LogP

-0.07

cLogP

Final rank

2.5550

rank score

Inter norm

-1.075

normalised

Contacts

H-bonds 16

Strain ΔE

47.7 kcal/mol

SASA buried

82%

Lipo contact

65% BSA apolar/total

SASA unbound

568 Å²

Apolar buried

306 Å²

Interaction summary

HBD 2 HBA 10 HY 4 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 7.

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: permissive.

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	5	HB role recall	0.56
HB same residue	5	HB residue recall	0.62

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
83	2.555017141541152	-1.07527	-25.6018	16	17	13	0.93	0.56	-	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 -25.602kcal/mol

Ligand efficiency (LE) -0.9482kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.847

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 369.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) -0.07

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 47.74kcal/mol

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

Docked FF energy 99.91kcal/mol

Minimised FF energy 52.17kcal/mol

SASA & burial

✓ computed

SASA (unbound) 567.9Å²

Total solvent-accessible surface area of free ligand

BSA total 467.4Å²

Buried surface area upon binding

BSA apolar 305.6Å²

Hydrophobic contacts buried

BSA polar 161.8Å²

Polar contacts buried

Fraction buried 82.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 65.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2141.9Å²

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 742.3Å²

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