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 MK25

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

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

16.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.75, Jaccard 0.50, H-bond role recall 1.00

Burial

53%

Hydrophobic fit

82%

Reason: 12 internal clashes

12 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (16/24 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. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.565 kcal/mol/HA) ✓ Good fit quality (FQ -5.45) ✓ Good H-bonds (4 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (16.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)

Score

-16.950

kcal/mol

-0.565

kcal/mol/HA

Fit Quality

-5.45

FQ (Leeson)

HAC

heavy atoms

412

LogP

4.16

cLogP

Final rank

2.5364

rank score

Inter norm

-0.622

normalised

Contacts

H-bonds 7

Strain ΔE

16.5 kcal/mol

SASA buried

53%

Lipo contact

82% BSA apolar/total

SASA unbound

718 Å²

Apolar buried

312 Å²

Interaction summary

HBD 3 HBA 1 HY 2 PI 1 CLASH 0

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

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: 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	0.50	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
300	2.536358449038341	-0.622233	-16.9495	7	10	6	0.75	1.00	-	no	Current
281	4.132600369931899	-0.882304	-24.1478	9	14	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 -16.950kcal/mol

Ligand efficiency (LE) -0.5650kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.450

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

Heavy atom count 30HA

Physicochemical properties

Molecular weight 411.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.16

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 16.48kcal/mol

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

Docked FF energy 23.40kcal/mol

Minimised FF energy 6.92kcal/mol

SASA & burial

✓ computed

SASA (unbound) 718.1Å²

Total solvent-accessible surface area of free ligand

BSA total 382.4Å²

Buried surface area upon binding

BSA apolar 312.5Å²

Hydrophobic contacts buried

BSA polar 70.0Å²

Polar contacts buried

Fraction buried 53.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 81.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3183.6Å²

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 1499.4Å²

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