Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand Z56799025

PDB6FXS↗

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

68.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

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

Burial

64%

Hydrophobic fit

63%

Reason: strain 68.1 kcal/mol

strain ΔE 68.1 kcal/mol 1 protein-contact clashes 67% of hydrophobic surface is solvent-exposed (14/21 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

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

B — Bioaccumulative (BCF>2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.916 kcal/mol/HA) ✓ Good fit quality (FQ -8.92) ✓ Good H-bonds (5 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Extreme strain energy (68.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-28.393

kcal/mol

-0.916

kcal/mol/HA

Fit Quality

-8.92

FQ (Leeson)

HAC

heavy atoms

449

LogP

6.13

cLogP

Final rank

2.2308

rank score

Inter norm

-0.875

normalised

Contacts

H-bonds 8

Strain ΔE

68.1 kcal/mol

SASA buried

64%

Lipo contact

63% BSA apolar/total

SASA unbound

724 Å²

Apolar buried

294 Å²

Interaction summary

HBA 5 HY 3 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	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	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
380	2.230768852820015	-0.874629	-28.3932	8	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 -28.393kcal/mol

Ligand efficiency (LE) -0.9159kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.923

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 449.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 6.13

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 68.14kcal/mol

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

Docked FF energy 62.86kcal/mol

Minimised FF energy -5.28kcal/mol

SASA & burial

✓ computed

SASA (unbound) 723.8Å²

Total solvent-accessible surface area of free ligand

BSA total 465.4Å²

Buried surface area upon binding

BSA apolar 294.4Å²

Hydrophobic contacts buried

BSA polar 171.1Å²

Polar contacts buried

Fraction buried 64.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 63.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2136.3Å²

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 796.9Å²

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