Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand Z56174576

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 mixed SASA done

Strain ΔE

15.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.52, Jaccard 0.38, H-bond role recall 0.36

Burial

81%

Hydrophobic fit

82%

Reason: 10 protein-contact clashes, 10 internal clashes

10 protein-contact clashes 10 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (9/19 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 (-1.040 kcal/mol/HA) ✓ Good fit quality (FQ -9.58) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (15.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-27.041

kcal/mol

-1.040

kcal/mol/HA

Fit Quality

-9.58

FQ (Leeson)

HAC

heavy atoms

370

LogP

3.76

cLogP

Final rank

4.2285

rank score

Inter norm

-1.167

normalised

Contacts

H-bonds 10

Strain ΔE

15.6 kcal/mol

SASA buried

81%

Lipo contact

82% BSA apolar/total

SASA unbound

581 Å²

Apolar buried

386 Å²

Interaction summary

HBD 1 HBA 5 HY 3 PI 0 CLASH 10

HBD/HBA · H-bonds (geometric)

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

PI · π–π interactions

No pi · π–π interactions detected for this pose.

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	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	11	Native recall	0.52
Jaccard	0.38	RMSD	-
HB strict	6	Strict recall	0.40
HB same residue+role	4	HB role recall	0.36
HB same residue	4	HB residue recall	0.36

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
373	2.1316147199863864	-1.24377	-30.4342	4	15	0	0.00	0.00	-	no	Open
394	4.228545575688243	-1.16663	-27.041	10	19	11	0.52	0.36	-	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 -27.041kcal/mol

Ligand efficiency (LE) -1.0400kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.582

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 370.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.76

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.55kcal/mol

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

Docked FF energy 6.21kcal/mol

Minimised FF energy -9.35kcal/mol

SASA & burial

✓ computed

SASA (unbound) 581.1Å²

Total solvent-accessible surface area of free ligand

BSA total 468.2Å²

Buried surface area upon binding

BSA apolar 386.2Å²

Hydrophobic contacts buried

BSA polar 82.0Å²

Polar contacts buried

Fraction buried 80.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 82.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1327.8Å²

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 512.3Å²

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