Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T11

L. infantum SIR2 L. infantum

Ligand Z25276890

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

15.4 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.72, Jaccard 0.62, H-bond role recall 0.20

Burial

77%

Hydrophobic fit

74%

Reason: 11 internal clashes

3 protein-contact clashes 11 intramolecular clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.408

ADMET + ECO + DL

ADMETscore (GDS)

0.444

absorption · distr. · metab.

DLscore

0.419

drug-likeness

P(SAFE)

0.14

GDS classification

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Risk

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.732 kcal/mol/HA) ✓ Good fit quality (FQ -7.13) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (15.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (11)

Score

-22.705

kcal/mol

-0.732

kcal/mol/HA

Fit Quality

-7.13

FQ (Leeson)

HAC

heavy atoms

430

LogP

4.43

cLogP

Final rank

1.0577

rank score

Inter norm

-0.798

normalised

Contacts

H-bonds 3

Strain ΔE

15.4 kcal/mol

SASA buried

77%

Lipo contact

74% BSA apolar/total

SASA unbound

699 Å²

Apolar buried

402 Å²

Interaction summary

HBA 2 HY 7 PI 4 CLASH 0

HBD/HBA · H-bonds (geometric)

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

Name	5OL0	Contacts	18
Pose	Open native pose	HB	0
IFP residues	ASN193 GLN220 GLU192 GLY191 HIS144 HIS222 ILE126 LEU194 LEU226 PHE189 PHE190 PHE199 PHE74 PRO223 THR71 VAL187 VAL188 VAL221
Current overlap	13	Native recall	0.72
Jaccard	0.62	RMSD	-
HB strict	1	Strict recall	0.20
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.25

Protein summary

287 residues

Protein target	T11	Atoms	4391
Residues	287	Chains	1
Residue summary	LEU:627; ARG:432; VAL:384; GLU:316; PHE:300; ILE:285; ALA:260; PRO:238; HIS:187; ASP:157; LYS:154; SER:154; THR:154; GLY:147; ASN:140; TYR:126

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
414	1.0577075427204725	-0.797735	-22.7049	3	16	13	0.72	0.20	-	no	Current
389	2.7193476055033234	-1.14467	-30.8585	11	20	0	0.00	0.00	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -22.705kcal/mol

Ligand efficiency (LE) -0.7324kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.135

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 430.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.43

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.40kcal/mol

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

Docked FF energy 25.64kcal/mol

Minimised FF energy 10.25kcal/mol

SASA & burial

✓ computed

SASA (unbound) 699.0Å²

Total solvent-accessible surface area of free ligand

BSA total 539.3Å²

Buried surface area upon binding

BSA apolar 401.9Å²

Hydrophobic contacts buried

BSA polar 137.4Å²

Polar contacts buried

Fraction buried 77.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 74.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1959.5Å²

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 2380.0Å²

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

Complex non-polar SASA 969.3Å²

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