Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand ulfkktlib_2087

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

48.8 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.76, H-bond role recall 0.78

Burial

75%

Hydrophobic fit

74%

Reason: strain 48.8 kcal/mol

strain ΔE 48.8 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 44% of hydrophobic surface appears solvent-exposed (8/18 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 Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.741 kcal/mol/HA) ✓ Good fit quality (FQ -6.82) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Extreme strain energy (48.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-19.253

kcal/mol

-0.741

kcal/mol/HA

Fit Quality

-6.82

FQ (Leeson)

HAC

heavy atoms

353

LogP

3.02

cLogP

Final rank

4.5587

rank score

Inter norm

-0.933

normalised

Contacts

H-bonds 15

Strain ΔE

48.8 kcal/mol

SASA buried

75%

Lipo contact

74% BSA apolar/total

SASA unbound

616 Å²

Apolar buried

342 Å²

Interaction summary

HBA 9 HY 2 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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	0.76	RMSD	-
HB strict	9	Strict recall	0.75
HB same residue+role	7	HB role recall	0.78
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
154	4.558711349686701	-0.932832	-19.2534	15	16	13	0.93	0.78	-	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 -19.253kcal/mol

Ligand efficiency (LE) -0.7405kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.823

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 353.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.02

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 48.81kcal/mol

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

Docked FF energy 57.55kcal/mol

Minimised FF energy 8.74kcal/mol

SASA & burial

✓ computed

SASA (unbound) 615.9Å²

Total solvent-accessible surface area of free ligand

BSA total 459.3Å²

Buried surface area upon binding

BSA apolar 342.3Å²

Hydrophobic contacts buried

BSA polar 117.0Å²

Polar contacts buried

Fraction buried 74.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 74.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2201.4Å²

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 767.3Å²

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