Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand Z28346745

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

24.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.76, Jaccard 0.73, H-bond role recall 0.45

Burial

72%

Hydrophobic fit

69%

Reason: 10 internal clashes

10 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (10/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model

ECOscore

0.485

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.433

ADMET + ECO + DL

ADMETscore (GDS)

0.403

absorption · distr. · metab.

DLscore

0.457

drug-likeness

P(SAFE)

0.83

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-1.442 kcal/mol/HA) ✓ Good fit quality (FQ -13.61) ✓ Good H-bonds (5 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ High strain energy (24.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)

Score

-40.375

kcal/mol

-1.442

kcal/mol/HA

Fit Quality

-13.61

FQ (Leeson)

HAC

heavy atoms

417

LogP

4.56

cLogP

Final rank

2.0852

rank score

Inter norm

-1.077

normalised

Contacts

H-bonds 10

Strain ΔE

24.9 kcal/mol

SASA buried

72%

Lipo contact

69% BSA apolar/total

SASA unbound

700 Å²

Apolar buried

348 Å²

Interaction summary

HBA 5 HY 2 PI 1 CLASH 0

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

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	RAB5A	Contacts	21
Pose	Open native pose	HB	0
IFP residues	ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap	16	Native recall	0.76
Jaccard	0.73	RMSD	-
HB strict	7	Strict recall	0.47
HB same residue+role	5	HB role recall	0.45
HB same residue	5	HB residue recall	0.45

Protein summary

165 residues

Protein target	T22	Atoms	2561
Residues	165	Chains	1
Residue summary	LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
467	2.0852073229209616	-1.07749	-40.3752	10	17	16	0.76	0.45	-	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 -40.375kcal/mol

Ligand efficiency (LE) -1.4420kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -13.613

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 416.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.56

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 24.87kcal/mol

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

Docked FF energy 52.65kcal/mol

Minimised FF energy 27.78kcal/mol

SASA & burial

✓ computed

SASA (unbound) 700.0Å²

Total solvent-accessible surface area of free ligand

BSA total 502.3Å²

Buried surface area upon binding

BSA apolar 348.2Å²

Hydrophobic contacts buried

BSA polar 154.1Å²

Polar contacts buried

Fraction buried 71.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 69.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1378.9Å²

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 1368.5Å²

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

Complex non-polar SASA 524.1Å²

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