Docking pose detail

Molecular metrics status: missing

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T22

L. donovani rab5a L. donovani

Ligand OHD_Leishmania_224

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak Metrics pending

Promising but geometrically suspicious

Binding strong Geometry low Native mixed SASA pending

Strain ΔE

121.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.48, Jaccard 0.37, H-bond role recall 0.36

Burial

Reason: strain 121.9 kcal/mol

strain ΔE 121.9 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (3/3 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

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Interaction summary

HBD 3 HBA 8 HY 0 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 7.

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: 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	10	Native recall	0.48
Jaccard	0.37	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
7	5.740453265440487	-2.87533	-34.9893	16	16	10	0.48	0.36	-	yes	Current

Molecular metrics

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

⚠ Not yet computed

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