Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand TC273

PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry high Native strong SASA done

Strain ΔE

20.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.88, H-bond role recall 0.50

Burial

70%

Hydrophobic fit

81%

Reason: no major geometry red flags detected

1 protein-contact clashes 44% of hydrophobic surface appears solvent-exposed (8/18 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 Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.895 kcal/mol/HA) ✓ Good fit quality (FQ -8.24) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (20.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-23.261

kcal/mol

-0.895

kcal/mol/HA

Fit Quality

-8.24

FQ (Leeson)

HAC

heavy atoms

362

LogP

2.56

cLogP

Final rank

2.2645

rank score

Inter norm

-1.046

normalised

Contacts

H-bonds 15

Strain ΔE

20.9 kcal/mol

SASA buried

70%

Lipo contact

81% BSA apolar/total

SASA unbound

700 Å²

Apolar buried

396 Å²

Interaction summary

HBA 7 HY 3 PI 4 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	6FXS	Contacts	16
Pose	Open native pose	HB	0
IFP residues	ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap	15	Native recall	0.94
Jaccard	0.88	RMSD	-
HB strict	7	Strict recall	0.58
HB same residue+role	5	HB role recall	0.50
HB same residue	5	HB residue recall	0.50

Protein summary

302 residues

Protein target	T12	Atoms	4598
Residues	302	Chains	2
Residue summary	ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
166	2.264520935232404	-1.04642	-23.2606	15	16	15	0.94	0.50	-	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 -23.261kcal/mol

Ligand efficiency (LE) -0.8946kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.243

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 362.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.56

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 20.88kcal/mol

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

Docked FF energy -17.62kcal/mol

Minimised FF energy -38.50kcal/mol

SASA & burial

✓ computed

SASA (unbound) 700.1Å²

Total solvent-accessible surface area of free ligand

BSA total 487.0Å²

Buried surface area upon binding

BSA apolar 396.1Å²

Hydrophobic contacts buried

BSA polar 90.9Å²

Polar contacts buried

Fraction buried 69.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 81.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2283.5Å²

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 2454.8Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 768.3Å²

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