Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T22

L. donovani rab5a L. donovani

Ligand OHD_TB2020_7

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

52.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.67, Jaccard 0.47, H-bond role recall 0.36

Burial

90%

Hydrophobic fit

73%

Reason: 8 internal clashes, strain 52.3 kcal/mol

strain ΔE 52.3 kcal/mol 8 protein-contact clashes 8 intramolecular clashes 55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

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 High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.943 kcal/mol/HA) ✓ Good fit quality (FQ -9.18) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Extreme strain energy (52.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-29.221

kcal/mol

-0.943

kcal/mol/HA

Fit Quality

-9.18

FQ (Leeson)

HAC

heavy atoms

458

LogP

4.27

cLogP

Final rank

4.0638

rank score

Inter norm

-1.088

normalised

Contacts

H-bonds 9

Strain ΔE

52.3 kcal/mol

SASA buried

90%

Lipo contact

73% BSA apolar/total

SASA unbound

712 Å²

Apolar buried

469 Å²

Interaction summary

HBA 6 HY 2 PI 0 CLASH 8

HBD/HBA · H-bonds (geometric)

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

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	0.47	RMSD	-
HB strict	6	Strict recall	0.40
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
20	4.063804428718616	-1.08763	-29.2205	9	23	14	0.67	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 -29.221kcal/mol

Ligand efficiency (LE) -0.9426kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.183

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 457.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.27

Lipinski: ≤ 5

Rotatable bonds 9

Conformational strain (MMFF94s)

Strain energy (ΔE) 52.28kcal/mol

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

Docked FF energy 52.00kcal/mol

Minimised FF energy -0.28kcal/mol

SASA & burial

✓ computed

SASA (unbound) 712.4Å²

Total solvent-accessible surface area of free ligand

BSA total 644.9Å²

Buried surface area upon binding

BSA apolar 469.0Å²

Hydrophobic contacts buried

BSA polar 175.9Å²

Polar contacts buried

Fraction buried 90.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 72.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1383.0Å²

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 500.0Å²

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