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 Z31271192

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

Likely artefact or unreliable pose

Binding strong Geometry medium Native strong SASA done

Strain ΔE

40.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.75, Jaccard 0.60, H-bond role recall 1.00

Burial

57%

Hydrophobic fit

76%

Reason: no major geometry red flags detected

1 protein-contact clashes 89% of hydrophobic surface is solvent-exposed (17/19 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 ↗

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

✓ Excellent LE (-0.777 kcal/mol/HA) ✓ Good fit quality (FQ -7.16) ✓ Good H-bonds (4 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Extreme strain energy (40.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)

Score

-20.204

kcal/mol

-0.777

kcal/mol/HA

Fit Quality

-7.16

FQ (Leeson)

HAC

heavy atoms

347

LogP

0.39

cLogP

Final rank

4.4452

rank score

Inter norm

-0.758

normalised

Contacts

H-bonds 5

Strain ΔE

40.7 kcal/mol

SASA buried

57%

Lipo contact

76% BSA apolar/total

SASA unbound

599 Å²

Apolar buried

261 Å²

Interaction summary

HBD 2 HBA 2 HY 1 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)

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

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	0.60	RMSD	-
HB strict	1	Strict recall	0.50
HB same residue+role	1	HB role recall	1.00
HB same residue	1	HB residue recall	1.00

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
408	4.445240340950495	-0.757698	-20.2038	5	8	6	0.75	1.00	-	no	Current
397	5.4938084297486	-0.869184	-18.9212	8	12	0	0.00	0.00	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -20.204kcal/mol

Ligand efficiency (LE) -0.7771kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.159

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 347.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.39

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 40.67kcal/mol

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

Docked FF energy 172.96kcal/mol

Minimised FF energy 132.28kcal/mol

SASA & burial

✓ computed

SASA (unbound) 599.4Å²

Total solvent-accessible surface area of free ligand

BSA total 341.8Å²

Buried surface area upon binding

BSA apolar 261.4Å²

Hydrophobic contacts buried

BSA polar 80.5Å²

Polar contacts buried

Fraction buried 57.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 76.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3051.5Å²

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 1512.9Å²

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