Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand KB_Leish_55

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

17.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.89, H-bond role recall 0.27

Burial

76%

Hydrophobic fit

91%

Reason: 9 protein-contact clashes, 9 internal clashes

9 protein-contact clashes 9 intramolecular clashes 39% of hydrophobic surface appears solvent-exposed (7/18 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 Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.845 kcal/mol/HA) ✓ Good fit quality (FQ -7.57) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Moderate strain (17.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-20.275

kcal/mol

-0.845

kcal/mol/HA

Fit Quality

-7.57

FQ (Leeson)

HAC

heavy atoms

340

LogP

4.02

cLogP

Final rank

4.6267

rank score

Inter norm

-1.017

normalised

Contacts

H-bonds 10

Strain ΔE

17.1 kcal/mol

SASA buried

76%

Lipo contact

91% BSA apolar/total

SASA unbound

595 Å²

Apolar buried

416 Å²

Interaction summary

HBA 7 HY 3 PI 2 CLASH 9

HBD/HBA · H-bonds (geometric)

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

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	6FXW	Contacts	17
Pose	Open native pose	HB	0
IFP residues	ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap	16	Native recall	0.94
Jaccard	0.89	RMSD	-
HB strict	4	Strict recall	0.31
HB same residue+role	3	HB role recall	0.27
HB same residue	3	HB residue recall	0.27

Protein summary

155 residues

Protein target	T10	Atoms	4590
Residues	155	Chains	1
Residue summary	ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
112	1.5242794877844776	-1.25534	-24.9001	2	15	0	0.00	0.00	-	no	Open
74	4.626660726424293	-1.01699	-20.2747	10	17	16	0.94	0.27	-	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 -20.275kcal/mol

Ligand efficiency (LE) -0.8448kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.571

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 339.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.02

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 17.14kcal/mol

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

Docked FF energy -0.79kcal/mol

Minimised FF energy -17.93kcal/mol

SASA & burial

✓ computed

SASA (unbound) 595.4Å²

Total solvent-accessible surface area of free ligand

BSA total 455.5Å²

Buried surface area upon binding

BSA apolar 416.0Å²

Hydrophobic contacts buried

BSA polar 39.5Å²

Polar contacts buried

Fraction buried 76.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 91.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2317.0Å²

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 2417.4Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 656.3Å²

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