Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand Z56983508

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry medium Native strong SASA done

Strain ΔE

36.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.95, Jaccard 0.77, H-bond role recall 0.45

Burial

89%

Hydrophobic fit

85%

Reason: no major geometry red flags detected

5 protein-contact clashes 5 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (11/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

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. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.858 kcal/mol/HA) ✓ Good fit quality (FQ -8.36) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Very high strain energy (36.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)

Score

-26.585

kcal/mol

-0.858

kcal/mol/HA

Fit Quality

-8.36

FQ (Leeson)

HAC

heavy atoms

466

LogP

3.06

cLogP

Final rank

4.7430

rank score

Inter norm

-0.989

normalised

Contacts

H-bonds 8

Strain ΔE

36.7 kcal/mol

SASA buried

89%

Lipo contact

85% BSA apolar/total

SASA unbound

727 Å²

Apolar buried

548 Å²

Interaction summary

HBA 6 HY 5 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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: 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	20	Native recall	0.95
Jaccard	0.77	RMSD	-
HB strict	6	Strict recall	0.40
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
564	2.603687598681537	-0.730592	-21.446	6	18	0	0.00	0.00	-	no	Open
549	4.743033425763289	-0.989041	-26.5847	8	25	20	0.95	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 -26.585kcal/mol

Ligand efficiency (LE) -0.8576kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.355

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 466.0Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.06

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 36.66kcal/mol

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

Docked FF energy 68.48kcal/mol

Minimised FF energy 31.82kcal/mol

SASA & burial

✓ computed

SASA (unbound) 727.2Å²

Total solvent-accessible surface area of free ligand

BSA total 648.3Å²

Buried surface area upon binding

BSA apolar 548.4Å²

Hydrophobic contacts buried

BSA polar 99.9Å²

Polar contacts buried

Fraction buried 89.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 84.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1484.9Å²

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 498.9Å²

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