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 CKP-45

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 mixed SASA done

Strain ΔE

6.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.54, Jaccard 0.37

Burial

70%

Hydrophobic fit

95%

Reason: no major geometry red flags detected

1 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 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.

✓ Low conformational strain (6.3 kcal/mol) ✓ Excellent LE (-0.891 kcal/mol/HA) ✓ Good fit quality (FQ -7.87) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (95%) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-20.496

kcal/mol

-0.891

kcal/mol/HA

Fit Quality

-7.87

FQ (Leeson)

HAC

heavy atoms

300

LogP

3.75

cLogP

Final rank

1.7062

rank score

Inter norm

-0.903

normalised

Contacts

H-bonds 2

Strain ΔE

6.3 kcal/mol

SASA buried

70%

Lipo contact

95% BSA apolar/total

SASA unbound

568 Å²

Apolar buried

376 Å²

Interaction summary

HBD 1 HY 6 PI 4 CLASH 1

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	7	Native recall	0.54
Jaccard	0.37	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
293	1.7062405716661662	-0.902953	-20.4957	2	13	7	0.54	-	-	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 -20.496kcal/mol

Ligand efficiency (LE) -0.8911kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.865

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 300.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.75

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 6.28kcal/mol

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

Docked FF energy 49.54kcal/mol

Minimised FF energy 43.26kcal/mol

SASA & burial

✓ computed

SASA (unbound) 567.5Å²

Total solvent-accessible surface area of free ligand

BSA total 394.4Å²

Buried surface area upon binding

BSA apolar 375.6Å²

Hydrophobic contacts buried

BSA polar 18.8Å²

Polar contacts buried

Fraction buried 69.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 95.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3141.6Å²

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 1480.5Å²

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