Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand Z26191442

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 medium Native strong SASA done

Strain ΔE

32.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.88, H-bond role recall 0.40

Burial

77%

Hydrophobic fit

77%

Reason: no major geometry red flags detected

2 protein-contact clashes 61% of hydrophobic surface is solvent-exposed (11/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.828 kcal/mol/HA) ✓ Good fit quality (FQ -7.63) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (32.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-21.529

kcal/mol

-0.828

kcal/mol/HA

Fit Quality

-7.63

FQ (Leeson)

HAC

heavy atoms

373

LogP

1.82

cLogP

Final rank

3.2940

rank score

Inter norm

-1.065

normalised

Contacts

H-bonds 7

Strain ΔE

32.1 kcal/mol

SASA buried

77%

Lipo contact

77% BSA apolar/total

SASA unbound

605 Å²

Apolar buried

359 Å²

Interaction summary

HBA 7 HY 4 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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: permissive.

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	6	Strict recall	0.50
HB same residue+role	4	HB role recall	0.40
HB same residue	4	HB residue recall	0.40

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
594	3.293997631105555	-1.0654	-21.5293	7	16	15	0.94	0.40	-	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 -21.529kcal/mol

Ligand efficiency (LE) -0.8280kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.629

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 373.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.82

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 32.12kcal/mol

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

Docked FF energy 97.66kcal/mol

Minimised FF energy 65.54kcal/mol

SASA & burial

✓ computed

SASA (unbound) 605.1Å²

Total solvent-accessible surface area of free ligand

BSA total 467.7Å²

Buried surface area upon binding

BSA apolar 359.3Å²

Hydrophobic contacts buried

BSA polar 108.4Å²

Polar contacts buried

Fraction buried 77.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 76.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2145.5Å²

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 776.7Å²

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