Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand Z45692840

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 high Native mixed SASA done

Strain ΔE

22.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.48, Jaccard 0.34, H-bond role recall 0.36

Burial

92%

Hydrophobic fit

82%

Reason: no major geometry red flags detected

2 protein-contact clashes 100% of hydrophobic surface is solvent-exposed (15/15 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. 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 ↗

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

✓ Excellent LE (-1.312 kcal/mol/HA) ✓ Good fit quality (FQ -11.19) ✓ Good H-bonds (5 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (22.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-27.560

kcal/mol

-1.312

kcal/mol/HA

Fit Quality

-11.19

FQ (Leeson)

HAC

heavy atoms

322

LogP

3.54

cLogP

Final rank

3.1179

rank score

Inter norm

-1.445

normalised

Contacts

H-bonds 6

Strain ΔE

22.9 kcal/mol

SASA buried

92%

Lipo contact

82% BSA apolar/total

SASA unbound

517 Å²

Apolar buried

390 Å²

Interaction summary

HBA 5 HY 0 PI 0 CLASH 2

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

No hy · hydrophobic contacts detected for this pose.

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	10	Native recall	0.48
Jaccard	0.34	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
392	3.117850156045787	-1.44452	-27.5598	6	18	10	0.48	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 -27.560kcal/mol

Ligand efficiency (LE) -1.3124kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.194

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 322.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.54

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 22.87kcal/mol

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

Docked FF energy 15.58kcal/mol

Minimised FF energy -7.29kcal/mol

SASA & burial

✓ computed

SASA (unbound) 516.8Å²

Total solvent-accessible surface area of free ligand

BSA total 477.8Å²

Buried surface area upon binding

BSA apolar 389.9Å²

Hydrophobic contacts buried

BSA polar 87.9Å²

Polar contacts buried

Fraction buried 92.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 81.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1289.2Å²

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 505.0Å²

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