Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T18

T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)

Ligand KB_Leish_187

PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising SASA cached

Promising and worth follow-up

Binding strong Geometry high Native strong SASA done

Strain ΔE

14.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.62, Jaccard 0.50

Burial

70%

Hydrophobic fit

82%

Reason: no major geometry red flags detected

1 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.875 kcal/mol/HA) ✓ Good fit quality (FQ -7.84) ✓ Good H-bonds (5 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (14.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-20.994

kcal/mol

-0.875

kcal/mol/HA

Fit Quality

-7.84

FQ (Leeson)

HAC

heavy atoms

344

LogP

2.71

cLogP

Final rank

2.8395

rank score

Inter norm

-0.920

normalised

Contacts

H-bonds 5

Strain ΔE

14.2 kcal/mol

SASA buried

70%

Lipo contact

82% BSA apolar/total

SASA unbound

599 Å²

Apolar buried

344 Å²

Interaction summary

HBD 2 HBA 3 HY 8 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

PI · π–π interactions

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	6RB5	Contacts	13
Pose	Open native pose	HB	0
IFP residues	ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap	8	Native recall	0.62
Jaccard	0.50	RMSD	-
HB strict	0	Strict recall	-
HB same residue+role	0	HB role recall	-
HB same residue	0	HB residue recall	-

Protein summary

493 residues

Protein target	T18	Atoms	7550
Residues	493	Chains	1
Residue summary	VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:FAD501

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
124	1.1269298578542286	-1.07845	-22.4414	6	16	0	0.00	-	-	no	Open
145	2.8394922375464198	-0.920162	-20.9943	5	11	8	0.62	-	-	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 -20.994kcal/mol

Ligand efficiency (LE) -0.8748kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.840

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 343.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.71

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 14.23kcal/mol

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

Docked FF energy 75.56kcal/mol

Minimised FF energy 61.33kcal/mol

SASA & burial

✓ computed

SASA (unbound) 599.0Å²

Total solvent-accessible surface area of free ligand

BSA total 420.5Å²

Buried surface area upon binding

BSA apolar 343.6Å²

Hydrophobic contacts buried

BSA polar 76.9Å²

Polar contacts buried

Fraction buried 70.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 81.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3078.2Å²

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 4076.6Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 1503.3Å²

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