Docking pose detail

Molecular metrics status: missing

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T22

L. donovani rab5a L. donovani

Ligand OHD_TB2022_29

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 strong SASA pending

Strain ΔE

67.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.71, Jaccard 0.71, H-bond role recall 0.64

Burial

50%

Reason: strain 67.3 kcal/mol

strain ΔE 67.3 kcal/mol 1 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Interaction summary

HB 13 HY 6 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 (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 12 Buried (contacted) 6 Exposed 6 LogP -1.58 H-bonds 13

Exposed fragments: aliphatic chain/group (6 atoms exposed)

Final rank	5.117	Score	-26.423
Inter norm	-1.307	Intra norm	0.250
Top1000	no	Excluded	yes
Contacts	15	H-bonds	13
Artifact reason	excluded; geometry warning; 6 clashes; 4 protein clashes; high strain Δ 67.3
Residues	ALA158 ALA24 ASN126 ASP129 GLU73 GLY23 GLY25 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28

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	15	Native recall	0.71
Jaccard	0.71	RMSD	-
HB strict	8	Strict recall	0.53
HB same residue+role	7	HB role recall	0.64
HB same residue	7	HB residue recall	0.64

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
40	5.116621655594289	-1.30718	-26.4234	13	15	15	0.71	0.64	-	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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