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_chagas_125

PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

55.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.85, Jaccard 0.61

Burial

64%

Hydrophobic fit

89%

Reason: strain 55.0 kcal/mol

strain ΔE 55.0 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 61% of hydrophobic surface is solvent-exposed (17/28 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

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.601 kcal/mol/HA) ✓ Good fit quality (FQ -6.06) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Extreme strain energy (55.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-21.033

kcal/mol

-0.601

kcal/mol/HA

Fit Quality

-6.06

FQ (Leeson)

HAC

heavy atoms

475

LogP

3.60

cLogP

Final rank

3.0763

rank score

Inter norm

-0.661

normalised

Contacts

H-bonds 5

Strain ΔE

55.0 kcal/mol

SASA buried

64%

Lipo contact

89% BSA apolar/total

SASA unbound

812 Å²

Apolar buried

464 Å²

Interaction summary

HBD 1 HBA 1 HY 6 PI 1 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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	11	Native recall	0.85
Jaccard	0.61	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
159	3.076314667740396	-0.661369	-21.0326	5	16	11	0.85	-	-	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 -21.033kcal/mol

Ligand efficiency (LE) -0.6009kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.061

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

Heavy atom count 35HA

Physicochemical properties

Molecular weight 474.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.60

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 54.96kcal/mol

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

Docked FF energy -10.71kcal/mol

Minimised FF energy -65.67kcal/mol

SASA & burial

✓ computed

SASA (unbound) 812.4Å²

Total solvent-accessible surface area of free ligand

BSA total 519.3Å²

Buried surface area upon binding

BSA apolar 464.3Å²

Hydrophobic contacts buried

BSA polar 55.0Å²

Polar contacts buried

Fraction buried 63.9%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 89.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3335.6Å²

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 1477.6Å²

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