Docking pose detail

Molecular metrics status: missing

Molecular metrics have not been computed yet for this pose.

No cached metrics

T22

L. donovani rab5a L. donovani

Ligand ulfkktlib_1802

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising Metrics pending

Promising and worth follow-up

Binding strong Geometry medium Native mixed SASA pending

Strain ΔE

not computed

Protein clashes

Internal clashes

Native overlap

contact recall 0.33, Jaccard 0.25, H-bond role recall 0.36

Burial

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (4/4 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

Interaction summary

HBD 3 HBA 10 HY 0 PI 0 CLASH 3

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	7	Native recall	0.33
Jaccard	0.25	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
179	3.6075433236390695	-2.73885	-30.0963	16	14	7	0.33	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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