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 Z56775559

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

42.4 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.85, Jaccard 0.55

Burial

69%

Hydrophobic fit

80%

Reason: strain 42.4 kcal/mol

strain ΔE 42.4 kcal/mol 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 High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.549 kcal/mol/HA) ✓ Good fit quality (FQ -5.87) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (42.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (27)

Score

-24.179

kcal/mol

-0.549

kcal/mol/HA

Fit Quality

-5.87

FQ (Leeson)

HAC

heavy atoms

595

LogP

4.52

cLogP

Final rank

2.7676

rank score

Inter norm

-0.480

normalised

Contacts

H-bonds 3

Strain ΔE

42.4 kcal/mol

SASA buried

69%

Lipo contact

80% BSA apolar/total

SASA unbound

932 Å²

Apolar buried

514 Å²

Interaction summary

HBA 2 HY 9 PI 2 CLASH 1

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

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	0.55	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
604	2.7675540002054433	-0.479909	-24.179	3	18	11	0.85	-	-	no	Current
593	4.106760461201954	-0.694753	-19.8214	8	21	0	0.00	-	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -24.179kcal/mol

Ligand efficiency (LE) -0.5495kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.872

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

Heavy atom count 44HA

Physicochemical properties

Molecular weight 594.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.52

Lipinski: ≤ 5

Rotatable bonds 10

Conformational strain (MMFF94s)

Strain energy (ΔE) 42.37kcal/mol

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

Docked FF energy 245.88kcal/mol

Minimised FF energy 203.52kcal/mol

SASA & burial

✓ computed

SASA (unbound) 932.1Å²

Total solvent-accessible surface area of free ligand

BSA total 642.7Å²

Buried surface area upon binding

BSA apolar 514.4Å²

Hydrophobic contacts buried

BSA polar 128.3Å²

Polar contacts buried

Fraction buried 69.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 80.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3310.4Å²

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 1520.9Å²

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