Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand KB_chagas_219

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

27.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.79, H-bond role recall 0.60

Burial

78%

Hydrophobic fit

87%

Reason: no major geometry red flags detected

1 protein-contact clashes

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

Yes

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 (-0.949 kcal/mol/HA) ✓ Good fit quality (FQ -9.06) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ High strain energy (27.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (9)

Score

-27.516

kcal/mol

-0.949

kcal/mol/HA

Fit Quality

-9.06

FQ (Leeson)

HAC

heavy atoms

401

LogP

2.59

cLogP

Final rank

1.3004

rank score

Inter norm

-0.968

normalised

Contacts

H-bonds 8

Strain ΔE

27.0 kcal/mol

SASA buried

78%

Lipo contact

87% BSA apolar/total

SASA unbound

626 Å²

Apolar buried

426 Å²

Interaction summary

HBD 2 HBA 5 HY 5 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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	0.79	RMSD	-
HB strict	6	Strict recall	0.50
HB same residue+role	6	HB role recall	0.60
HB same residue	6	HB residue recall	0.60

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
121	1.3004228751437215	-0.968212	-27.5158	8	18	15	0.94	0.60	-	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 -27.516kcal/mol

Ligand efficiency (LE) -0.9488kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.057

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

Heavy atom count 29HA

Physicochemical properties

Molecular weight 401.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.59

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 27.04kcal/mol

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

Docked FF energy 0.19kcal/mol

Minimised FF energy -26.85kcal/mol

SASA & burial

✓ computed

SASA (unbound) 625.9Å²

Total solvent-accessible surface area of free ligand

BSA total 490.5Å²

Buried surface area upon binding

BSA apolar 426.0Å²

Hydrophobic contacts buried

BSA polar 64.5Å²

Polar contacts buried

Fraction buried 78.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 86.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2189.9Å²

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 823.1Å²

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