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 Z68348244

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

79.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.88, Jaccard 0.78, H-bond role recall 0.00

Burial

50%

Hydrophobic fit

75%

Reason: 8 internal clashes, strain 79.1 kcal/mol

strain ΔE 79.1 kcal/mol 8 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (9/16 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

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 ↗

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

✓ Excellent LE (-0.730 kcal/mol/HA) ✓ Good fit quality (FQ -6.81) ✓ Good H-bonds (5 bonds) ✓ Good burial (50% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (79.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-19.708

kcal/mol

-0.730

kcal/mol/HA

Fit Quality

-6.81

FQ (Leeson)

HAC

heavy atoms

432

LogP

1.75

cLogP

Final rank

3.0620

rank score

Inter norm

-0.776

normalised

Contacts

H-bonds 8

Strain ΔE

79.1 kcal/mol

SASA buried

50%

Lipo contact

75% BSA apolar/total

SASA unbound

609 Å²

Apolar buried

227 Å²

Interaction summary

HBD 2 HBA 3 HY 2 PI 1 CLASH 0

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

No clash · clashes detected for this pose.

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	7	Native recall	0.88
Jaccard	0.78	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
473	1.837370445853712	-1.14723	-30.851	10	21	0	0.00	0.00	-	no	Open
498	3.0620227767216486	-0.776394	-19.7079	8	8	7	0.88	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 -19.708kcal/mol

Ligand efficiency (LE) -0.7299kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.810

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 432.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.75

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 79.05kcal/mol

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

Docked FF energy 76.21kcal/mol

Minimised FF energy -2.84kcal/mol

SASA & burial

✓ computed

SASA (unbound) 609.0Å²

Total solvent-accessible surface area of free ligand

BSA total 302.1Å²

Buried surface area upon binding

BSA apolar 226.6Å²

Hydrophobic contacts buried

BSA polar 75.5Å²

Polar contacts buried

Fraction buried 49.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 75.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2972.6Å²

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 1564.8Å²

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