Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T20

T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)

Ligand Z25747797

PDB9IFH↗

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

46.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00

Burial

59%

Hydrophobic fit

77%

Reason: strain 46.9 kcal/mol

strain ΔE 46.9 kcal/mol 1 protein-contact clashes 47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>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 ↗

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

✓ Excellent LE (-1.382 kcal/mol/HA) ✓ Good fit quality (FQ -13.05) ✓ Good H-bonds (4 bonds) ✓ Good burial (59% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Extreme strain energy (46.9 kcal/mol) ✗ Geometry warnings

Score

-38.699

kcal/mol

-1.382

kcal/mol/HA

Fit Quality

-13.05

FQ (Leeson)

HAC

heavy atoms

404

LogP

2.42

cLogP

Final rank

3.9716

rank score

Inter norm

-0.673

normalised

Contacts

H-bonds 5

Strain ΔE

46.9 kcal/mol

SASA buried

59%

Lipo contact

77% BSA apolar/total

SASA unbound

636 Å²

Apolar buried

290 Å²

Interaction summary

HBD 2 HBA 2 HY 5 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)

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

PI · π–π interactions

No pi · π–π interactions detected for this pose.

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	9IFH	Contacts	8
Pose	Open native pose	HB	0
IFP residues	ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap	6	Native recall	0.75
Jaccard	0.43	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	0	HB residue recall	0.00

Protein summary

492 residues

Protein target	T20	Atoms	7539
Residues	492	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:264; 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
652	1.9994636660261382	-0.909597	-38.3936	5	16	0	0.00	0.00	-	no	Open
671	3.9715866745451636	-0.673163	-38.6986	5	12	6	0.75	0.00	-	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 -38.699kcal/mol

Ligand efficiency (LE) -1.3821kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -13.047

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

Heavy atom count 28HA

Physicochemical properties

Molecular weight 404.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.42

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 46.87kcal/mol

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

Docked FF energy -5.10kcal/mol

Minimised FF energy -51.98kcal/mol

SASA & burial

✓ computed

SASA (unbound) 636.1Å²

Total solvent-accessible surface area of free ligand

BSA total 376.2Å²

Buried surface area upon binding

BSA apolar 290.1Å²

Hydrophobic contacts buried

BSA polar 86.1Å²

Polar contacts buried

Fraction buried 59.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 77.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3091.5Å²

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 4069.8Å²

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

Complex non-polar SASA 1470.9Å²

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