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 OHD_TB2021_63

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

49.8 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.85, Jaccard 0.48

Burial

72%

Hydrophobic fit

93%

Reason: 21 internal clashes, strain 49.8 kcal/mol

strain ΔE 49.8 kcal/mol 21 intramolecular 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 High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.496 kcal/mol/HA) ✓ Good fit quality (FQ -5.08) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ Extreme strain energy (49.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (21)

Score

-18.346

kcal/mol

-0.496

kcal/mol/HA

Fit Quality

-5.08

FQ (Leeson)

HAC

heavy atoms

494

LogP

4.48

cLogP

Final rank

2.9962

rank score

Inter norm

-0.608

normalised

Contacts

H-bonds 5

Strain ΔE

49.8 kcal/mol

SASA buried

72%

Lipo contact

93% BSA apolar/total

SASA unbound

889 Å²

Apolar buried

598 Å²

Interaction summary

HBD 2 HY 8 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions

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

HY · Hydrophobic contacts

CLASH · Clashes

No clash · clashes detected for this pose.

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	0.48	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
52	2.996249908623322	-0.607988	-18.3462	5	21	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 -18.346kcal/mol

Ligand efficiency (LE) -0.4958kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.076

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

Heavy atom count 37HA

Physicochemical properties

Molecular weight 493.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.48

Lipinski: ≤ 5

Rotatable bonds 12

Conformational strain (MMFF94s)

Strain energy (ΔE) 49.82kcal/mol

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

Docked FF energy 57.75kcal/mol

Minimised FF energy 7.93kcal/mol

SASA & burial

✓ computed

SASA (unbound) 889.0Å²

Total solvent-accessible surface area of free ligand

BSA total 640.8Å²

Buried surface area upon binding

BSA apolar 597.9Å²

Hydrophobic contacts buried

BSA polar 42.9Å²

Polar contacts buried

Fraction buried 72.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 93.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3388.1Å²

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 1507.3Å²

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