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 MK4

PDB9IFH↗

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

23.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.62, Jaccard 0.29, H-bond role recall 0.00

Burial

54%

Hydrophobic fit

79%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes 63% of hydrophobic surface is solvent-exposed (17/27 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. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.613 kcal/mol/HA) ✓ Good fit quality (FQ -6.18) ✓ Strong H-bond network (6 bonds) ✓ Good burial (54% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (23.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)

Score

-21.451

kcal/mol

-0.613

kcal/mol/HA

Fit Quality

-6.18

FQ (Leeson)

HAC

heavy atoms

481

LogP

3.20

cLogP

Final rank

3.6667

rank score

Inter norm

-0.736

normalised

Contacts

H-bonds 9

Strain ΔE

23.7 kcal/mol

SASA buried

54%

Lipo contact

79% BSA apolar/total

SASA unbound

776 Å²

Apolar buried

332 Å²

Interaction summary

HBD 2 HBA 4 HY 2 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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	5	Native recall	0.62
Jaccard	0.29	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
294	3.6666599457801454	-0.736196	-21.4506	9	14	5	0.62	0.00	-	no	Current
348	3.799190168096806	-0.730489	-21.4664	6	17	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 -21.451kcal/mol

Ligand efficiency (LE) -0.6129kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.182

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

Heavy atom count 35HA

Physicochemical properties

Molecular weight 480.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.20

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 23.65kcal/mol

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

Docked FF energy 100.92kcal/mol

Minimised FF energy 77.27kcal/mol

SASA & burial

✓ computed

SASA (unbound) 776.2Å²

Total solvent-accessible surface area of free ligand

BSA total 421.8Å²

Buried surface area upon binding

BSA apolar 332.2Å²

Hydrophobic contacts buried

BSA polar 89.6Å²

Polar contacts buried

Fraction buried 54.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 78.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3197.9Å²

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 1515.1Å²

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