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 Z56890899

PDB6RB5↗

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

32.8 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.58, Jaccard 0.32

Burial

78%

Hydrophobic fit

82%

Reason: no major geometry red flags detected

2 protein-contact clashes

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 (-0.764 kcal/mol/HA) ✓ Good fit quality (FQ -7.37) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (32.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)

Score

-22.927

kcal/mol

-0.764

kcal/mol/HA

Fit Quality

-7.37

FQ (Leeson)

HAC

heavy atoms

418

LogP

4.07

cLogP

Final rank

2.6360

rank score

Inter norm

-0.764

normalised

Contacts

H-bonds 2

Strain ΔE

32.8 kcal/mol

SASA buried

78%

Lipo contact

82% BSA apolar/total

SASA unbound

684 Å²

Apolar buried

440 Å²

Interaction summary

HBA 2 HY 9 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

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	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	7	Native recall	0.58
Jaccard	0.32	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
489	2.636037679981359	-0.764182	-22.927	2	17	7	0.58	-	-	no	Current
386	4.110089435729965	-0.916695	-22.3096	8	17	0	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 -22.927kcal/mol

Ligand efficiency (LE) -0.7642kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.372

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

Heavy atom count 30HA

Physicochemical properties

Molecular weight 418.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.07

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 32.80kcal/mol

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

Docked FF energy 91.58kcal/mol

Minimised FF energy 58.78kcal/mol

SASA & burial

✓ computed

SASA (unbound) 684.2Å²

Total solvent-accessible surface area of free ligand

BSA total 536.3Å²

Buried surface area upon binding

BSA apolar 439.9Å²

Hydrophobic contacts buried

BSA polar 96.5Å²

Polar contacts buried

Fraction buried 78.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 82.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3161.7Å²

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 1479.2Å²

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