Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand KB_Leish_46

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

45.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.81, Jaccard 0.71, H-bond role recall 0.36

Burial

84%

Hydrophobic fit

84%

Reason: strain 45.9 kcal/mol

strain ΔE 45.9 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 71% of hydrophobic surface is solvent-exposed (17/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

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. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.883 kcal/mol/HA) ✓ Good fit quality (FQ -8.68) ✓ Good H-bonds (5 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (45.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)

Score

-28.255

kcal/mol

-0.883

kcal/mol/HA

Fit Quality

-8.68

FQ (Leeson)

HAC

heavy atoms

478

LogP

3.61

cLogP

Final rank

3.8403

rank score

Inter norm

-1.020

normalised

Contacts

H-bonds 6

Strain ΔE

45.9 kcal/mol

SASA buried

84%

Lipo contact

84% BSA apolar/total

SASA unbound

693 Å²

Apolar buried

489 Å²

Interaction summary

HBD 1 HBA 4 HY 2 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)

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

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	17	Native recall	0.81
Jaccard	0.71	RMSD	-
HB strict	5	Strict recall	0.33
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
140	2.801213136677595	-0.925317	-25.6492	3	14	0	0.00	0.00	-	no	Open
154	3.198430692215305	-0.587023	-19.525	2	13	0	0.00	0.00	-	no	Open
92	3.8403208941305516	-1.02026	-28.2546	6	20	17	0.81	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 -28.255kcal/mol

Ligand efficiency (LE) -0.8830kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.683

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

Heavy atom count 32HA

Physicochemical properties

Molecular weight 478.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.61

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 45.86kcal/mol

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

Docked FF energy 98.23kcal/mol

Minimised FF energy 52.37kcal/mol

SASA & burial

✓ computed

SASA (unbound) 692.8Å²

Total solvent-accessible surface area of free ligand

BSA total 583.6Å²

Buried surface area upon binding

BSA apolar 488.8Å²

Hydrophobic contacts buried

BSA polar 94.8Å²

Polar contacts buried

Fraction buried 84.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 83.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1459.1Å²

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 506.9Å²

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