Docking pose detail

Molecular metrics status: missing

Molecular metrics have not been computed yet for this pose.

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T22

L. donovani rab5a L. donovani

Ligand Z275145784

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 high Native strong SASA pending

Strain ΔE

not computed

Protein clashes

Internal clashes

Native overlap

contact recall 0.62, Jaccard 0.59, H-bond role recall 0.55

Burial

50%

Reason: no major geometry red flags detected

1 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (7/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Interaction summary

HB 13 HY 1 PI 1 CLASH 1 ⚠ Exposure 50%

HB · H-bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

⚠️Partial hydrophobic solvent exposure

50% of hydrophobic surface appears solvent-exposed (7/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 14 Buried (contacted) 7 Exposed 7 LogP 0.14 H-bonds 13

Exposed fragments: phenyl (2/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)

Final rank	5.627	Score	-33.466
Inter norm	-1.280	Intra norm	-0.007
Top1000	no	Excluded	yes
Contacts	14	H-bonds	13
Artifact reason	excluded; geometry warning; 6 clashes; 5 protein clashes
Residues	ALA158 ALA24 ALA40 ASN126 ASN41 GLY23 GLY25 LYS127 LYS159 LYS26 PHE38 SER27 SER28 THR44

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	13	Native recall	0.62
Jaccard	0.59	RMSD	-
HB strict	7	Strict recall	0.47
HB same residue+role	6	HB role recall	0.55
HB same residue	6	HB residue recall	0.55

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
554	5.626652983510588	-1.27978	-33.4664	13	14	13	0.62	0.55	-	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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