Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand Z31453186

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

28.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.76, Jaccard 0.55, H-bond role recall 0.36

Burial

89%

Hydrophobic fit

86%

Reason: 10 protein-contact clashes, 10 internal clashes

10 protein-contact clashes 10 intramolecular clashes 75% of hydrophobic surface is solvent-exposed (15/20 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. 3 — Harmful (10–100 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 (-1.036 kcal/mol/HA) ✓ Good fit quality (FQ -9.89) ✓ Good H-bonds (5 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (28.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-30.050

kcal/mol

-1.036

kcal/mol/HA

Fit Quality

-9.89

FQ (Leeson)

HAC

heavy atoms

441

LogP

3.21

cLogP

Final rank

5.0960

rank score

Inter norm

-1.053

normalised

Contacts

H-bonds 7

Strain ΔE

28.0 kcal/mol

SASA buried

89%

Lipo contact

86% BSA apolar/total

SASA unbound

696 Å²

Apolar buried

531 Å²

Interaction summary

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	16	Native recall	0.76
Jaccard	0.55	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
486	3.8178149116807925	-0.940835	-22.4221	8	16	0	0.00	0.00	-	no	Open
504	5.095964067331826	-1.05278	-30.0502	7	24	16	0.76	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 -30.050kcal/mol

Ligand efficiency (LE) -1.0362kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.891

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

Heavy atom count 29HA

Physicochemical properties

Molecular weight 440.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.21

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 28.02kcal/mol

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

Docked FF energy -11.09kcal/mol

Minimised FF energy -39.11kcal/mol

SASA & burial

✓ computed

SASA (unbound) 696.5Å²

Total solvent-accessible surface area of free ligand

BSA total 617.9Å²

Buried surface area upon binding

BSA apolar 531.3Å²

Hydrophobic contacts buried

BSA polar 86.7Å²

Polar contacts buried

Fraction buried 88.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 86.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1455.8Å²

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 506.5Å²

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