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_Leishmania_113

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

55.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.85, Jaccard 0.65

Burial

58%

Hydrophobic fit

89%

Reason: strain 55.6 kcal/mol

strain ΔE 55.6 kcal/mol 1 protein-contact clashes 43% of hydrophobic surface appears solvent-exposed (16/37 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

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 High Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.421 kcal/mol/HA) ✓ Good fit quality (FQ -4.65) ✓ Good H-bonds (3 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Extreme strain energy (55.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)

Score

-21.472

kcal/mol

-0.421

kcal/mol/HA

Fit Quality

-4.65

FQ (Leeson)

HAC

heavy atoms

702

LogP

3.28

cLogP

Final rank

4.3634

rank score

Inter norm

-0.448

normalised

Contacts

H-bonds 5

Strain ΔE

55.6 kcal/mol

SASA buried

58%

Lipo contact

89% BSA apolar/total

SASA unbound

1021 Å²

Apolar buried

523 Å²

Interaction summary

HBD 2 HBA 1 HY 9 PI 2 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	11	Native recall	0.85
Jaccard	0.65	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
3	4.363358870317496	-0.448166	-21.4724	5	15	11	0.85	-	-	no	Current
5	4.8177919206057345	-0.436816	-18.4401	5	22	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 -21.472kcal/mol

Ligand efficiency (LE) -0.4210kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.646

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

Heavy atom count 51HA

Physicochemical properties

Molecular weight 701.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.28

Lipinski: ≤ 5

Rotatable bonds 13

Conformational strain (MMFF94s)

Strain energy (ΔE) 55.59kcal/mol

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

Docked FF energy 215.75kcal/mol

Minimised FF energy 160.16kcal/mol

SASA & burial

✓ computed

SASA (unbound) 1020.6Å²

Total solvent-accessible surface area of free ligand

BSA total 587.5Å²

Buried surface area upon binding

BSA apolar 523.0Å²

Hydrophobic contacts buried

BSA polar 64.4Å²

Polar contacts buried

Fraction buried 57.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 89.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3441.5Å²

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 1542.1Å²

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