Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand OSA_Lib_227

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

49.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.67, Jaccard 0.56, H-bond role recall 0.00

Burial

79%

Hydrophobic fit

100%

Reason: strain 49.9 kcal/mol

strain ΔE 49.9 kcal/mol 1 protein-contact clashes 69% of hydrophobic surface is solvent-exposed (22/32 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

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.738 kcal/mol/HA) ✓ Good fit quality (FQ -7.50) ✓ Good H-bonds (3 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (100%) ✗ Extreme strain energy (49.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)

Score

-26.551

kcal/mol

-0.738

kcal/mol/HA

Fit Quality

-7.50

FQ (Leeson)

HAC

heavy atoms

490

LogP

0.64

cLogP

Final rank

2.4420

rank score

Inter norm

-0.856

normalised

Contacts

H-bonds 3

Strain ΔE

49.9 kcal/mol

SASA buried

79%

Lipo contact

100% BSA apolar/total

SASA unbound

815 Å²

Apolar buried

638 Å²

Interaction summary

HBD 3 HY 3 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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	14	Native recall	0.67
Jaccard	0.56	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	1	HB residue recall	0.09

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
156	2.4420009069038358	-0.856316	-26.5506	3	18	14	0.67	0.00	-	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 -26.551kcal/mol

Ligand efficiency (LE) -0.7375kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.496

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

Heavy atom count 36HA

Physicochemical properties

Molecular weight 489.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.64

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 49.95kcal/mol

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

Docked FF energy 363.65kcal/mol

Minimised FF energy 313.71kcal/mol

SASA & burial

✓ computed

SASA (unbound) 814.5Å²

Total solvent-accessible surface area of free ligand

BSA total 641.1Å²

Buried surface area upon binding

BSA apolar 637.9Å²

Hydrophobic contacts buried

BSA polar 3.2Å²

Polar contacts buried

Fraction buried 78.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 99.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1675.2Å²

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 501.6Å²

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