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 Z56827130

PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

42.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.83, Jaccard 0.50

Burial

73%

Hydrophobic fit

95%

Reason: strain 42.1 kcal/mol

strain ΔE 42.1 kcal/mol 1 protein-contact clashes 39% of hydrophobic surface appears solvent-exposed (12/31 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

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 High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.436 kcal/mol/HA) ✓ Good fit quality (FQ -4.46) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (95%) ✗ Extreme strain energy (42.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)

Score

-16.133

kcal/mol

-0.436

kcal/mol/HA

Fit Quality

-4.46

FQ (Leeson)

HAC

heavy atoms

497

LogP

4.27

cLogP

Final rank

2.5768

rank score

Inter norm

-0.640

normalised

Contacts

H-bonds 3

Strain ΔE

42.1 kcal/mol

SASA buried

73%

Lipo contact

95% BSA apolar/total

SASA unbound

849 Å²

Apolar buried

587 Å²

Interaction summary

HBD 1 HBA 1 HY 8 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)

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

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	10	Native recall	0.83
Jaccard	0.50	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
567	2.576768874667972	-0.640206	-16.1331	3	18	10	0.83	-	-	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 -16.133kcal/mol

Ligand efficiency (LE) -0.4360kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.464

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

Heavy atom count 37HA

Physicochemical properties

Molecular weight 496.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.27

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 42.10kcal/mol

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

Docked FF energy 216.88kcal/mol

Minimised FF energy 174.78kcal/mol

SASA & burial

✓ computed

SASA (unbound) 848.9Å²

Total solvent-accessible surface area of free ligand

BSA total 617.8Å²

Buried surface area upon binding

BSA apolar 586.7Å²

Hydrophobic contacts buried

BSA polar 31.1Å²

Polar contacts buried

Fraction buried 72.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 95.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3421.0Å²

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 1467.9Å²

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