Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand ulfkktlib_3920

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

46.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.67, Jaccard 0.48, H-bond role recall 0.27

Burial

85%

Hydrophobic fit

90%

Reason: 6 internal clashes, strain 46.7 kcal/mol

strain ΔE 46.7 kcal/mol 6 protein-contact clashes 6 intramolecular clashes 75% of hydrophobic surface is solvent-exposed (18/24 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. 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

Yes

ADMET alerts (in-silico)

hERG High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.888 kcal/mol/HA) ✓ Good fit quality (FQ -8.81) ✓ Good H-bonds (5 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (46.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)

Score

-29.312

kcal/mol

-0.888

kcal/mol/HA

Fit Quality

-8.81

FQ (Leeson)

HAC

heavy atoms

483

LogP

4.30

cLogP

Final rank

4.4021

rank score

Inter norm

-0.950

normalised

Contacts

H-bonds 6

Strain ΔE

46.7 kcal/mol

SASA buried

85%

Lipo contact

90% BSA apolar/total

SASA unbound

629 Å²

Apolar buried

486 Å²

Interaction summary

HBD 1 HBA 4 HY 1 PI 0 CLASH 6

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: 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	14	Native recall	0.67
Jaccard	0.48	RMSD	-
HB strict	4	Strict recall	0.27
HB same residue+role	3	HB role recall	0.27
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
190	4.402093266235169	-0.9497	-29.3124	6	22	14	0.67	0.27	-	no	Current
255	4.846945119501908	-0.659699	-22.085	5	7	0	0.00	0.00	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -29.312kcal/mol

Ligand efficiency (LE) -0.8883kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.813

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 482.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.30

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 46.72kcal/mol

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

Docked FF energy 66.33kcal/mol

Minimised FF energy 19.61kcal/mol

SASA & burial

✓ computed

SASA (unbound) 629.3Å²

Total solvent-accessible surface area of free ligand

BSA total 537.0Å²

Buried surface area upon binding

BSA apolar 485.6Å²

Hydrophobic contacts buried

BSA polar 51.5Å²

Polar contacts buried

Fraction buried 85.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 90.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1419.8Å²

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 526.6Å²

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