Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T16

T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)

Ligand Z56845221

PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising SASA cached

Promising and worth follow-up

Binding strong Geometry medium Native mixed SASA done

Strain ΔE

11.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.42, Jaccard 0.26

Burial

69%

Hydrophobic fit

62%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes

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 ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.335 kcal/mol/HA) ✓ Good fit quality (FQ -10.94) ✓ Good H-bonds (3 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Moderate strain (11.2 kcal/mol) ✗ Geometry warnings

Score

-25.357

kcal/mol

-1.335

kcal/mol/HA

Fit Quality

-10.94

FQ (Leeson)

HAC

heavy atoms

310

LogP

2.33

cLogP

Final rank

1.6325

rank score

Inter norm

-1.198

normalised

Contacts

H-bonds 6

Strain ΔE

11.2 kcal/mol

SASA buried

69%

Lipo contact

62% BSA apolar/total

SASA unbound

529 Å²

Apolar buried

226 Å²

Interaction summary

HBD 2 HBA 1 HY 5 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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: permissive.

Name	6RB5	Contacts	12
Pose	Open native pose	HB	0
IFP residues	ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap	5	Native recall	0.42
Jaccard	0.26	RMSD	-
HB strict	0	Strict recall	-
HB same residue+role	0	HB role recall	-
HB same residue	0	HB residue recall	-

Protein summary

493 residues

Protein target	T16	Atoms	7551
Residues	493	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:276; 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
644	1.632454308911163	-1.1979	-25.3566	6	12	5	0.42	-	-	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 -25.357kcal/mol

Ligand efficiency (LE) -1.3346kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.939

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

Heavy atom count 19HA

Physicochemical properties

Molecular weight 310.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.33

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 11.18kcal/mol

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

Docked FF energy 76.83kcal/mol

Minimised FF energy 65.65kcal/mol

SASA & burial

✓ computed

SASA (unbound) 529.1Å²

Total solvent-accessible surface area of free ligand

BSA total 363.8Å²

Buried surface area upon binding

BSA apolar 226.4Å²

Hydrophobic contacts buried

BSA polar 137.4Å²

Polar contacts buried

Fraction buried 68.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 62.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2983.9Å²

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 4076.6Å²

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

Complex non-polar SASA 1466.1Å²

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