Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand OHD_TC1_139

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 and worth follow-up

Binding strong Geometry high Native mixed SASA done

Strain ΔE

16.4 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.50, Jaccard 0.47, H-bond role recall 0.22

Burial

69%

Hydrophobic fit

77%

Reason: no major geometry red flags detected

2 protein-contact clashes 56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

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. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.992 kcal/mol/HA) ✓ Good fit quality (FQ -8.46) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (16.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-20.829

kcal/mol

-0.992

kcal/mol/HA

Fit Quality

-8.46

FQ (Leeson)

HAC

heavy atoms

279

LogP

2.88

cLogP

Final rank

4.2167

rank score

Inter norm

-1.176

normalised

Contacts

H-bonds 10

Strain ΔE

16.4 kcal/mol

SASA buried

69%

Lipo contact

77% BSA apolar/total

SASA unbound

518 Å²

Apolar buried

273 Å²

Interaction summary

HBD 1 HBA 6 HY 1 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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	7	Native recall	0.50
Jaccard	0.47	RMSD	-
HB strict	4	Strict recall	0.33
HB same residue+role	2	HB role recall	0.22
HB same residue	2	HB residue recall	0.25

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
36	3.0144044091666906	-1.30376	-21.2924	9	14	0	0.00	0.00	-	no	Open
64	4.216724923599552	-1.17602	-20.829	10	8	7	0.50	0.22	-	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 -20.829kcal/mol

Ligand efficiency (LE) -0.9919kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.460

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 279.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.88

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 16.43kcal/mol

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

Docked FF energy 25.21kcal/mol

Minimised FF energy 8.78kcal/mol

SASA & burial

✓ computed

SASA (unbound) 517.6Å²

Total solvent-accessible surface area of free ligand

BSA total 356.1Å²

Buried surface area upon binding

BSA apolar 273.2Å²

Hydrophobic contacts buried

BSA polar 82.9Å²

Polar contacts buried

Fraction buried 68.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 76.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2142.0Å²

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 768.8Å²

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