Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand MK61

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

41.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.59, H-bond role recall 0.33

Burial

74%

Hydrophobic fit

88%

Reason: 16 internal clashes

16 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (11/29 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. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.514 kcal/mol/HA) ✓ Good fit quality (FQ -5.22) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Extreme strain energy (41.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-18.501

kcal/mol

-0.514

kcal/mol/HA

Fit Quality

-5.22

FQ (Leeson)

HAC

heavy atoms

495

LogP

3.93

cLogP

Final rank

2.7121

rank score

Inter norm

-0.672

normalised

Contacts

H-bonds 5

Strain ΔE

41.1 kcal/mol

SASA buried

74%

Lipo contact

88% BSA apolar/total

SASA unbound

805 Å²

Apolar buried

522 Å²

Interaction summary

HBD 1 HBA 2 HY 3 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions

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

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	0.59	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
265	2.712069681419694	-0.671887	-18.5013	5	21	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 -18.501kcal/mol

Ligand efficiency (LE) -0.5139kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.223

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

Heavy atom count 36HA

Physicochemical properties

Molecular weight 494.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.93

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 41.10kcal/mol

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

Docked FF energy 184.85kcal/mol

Minimised FF energy 143.75kcal/mol

SASA & burial

✓ computed

SASA (unbound) 805.1Å²

Total solvent-accessible surface area of free ligand

BSA total 594.6Å²

Buried surface area upon binding

BSA apolar 522.2Å²

Hydrophobic contacts buried

BSA polar 72.4Å²

Polar contacts buried

Fraction buried 73.9%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 87.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2433.6Å²

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 736.9Å²

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