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 Z49558969

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 but geometrically suspicious

Binding strong Geometry low Native mixed SASA done

Strain ΔE

7.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.42, Jaccard 0.26

Burial

65%

Hydrophobic fit

77%

Reason: 7 internal clashes

7 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (9/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

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 Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Low conformational strain (7.9 kcal/mol) ✓ Excellent LE (-1.074 kcal/mol/HA) ✓ Good fit quality (FQ -9.77) ✓ Good H-bonds (4 bonds) ✓ Good burial (65% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-26.855

kcal/mol

-1.074

kcal/mol/HA

Fit Quality

-9.77

FQ (Leeson)

HAC

heavy atoms

338

LogP

2.54

cLogP

Final rank

3.4693

rank score

Inter norm

-1.065

normalised

Contacts

H-bonds 5

Strain ΔE

7.9 kcal/mol

SASA buried

65%

Lipo contact

77% BSA apolar/total

SASA unbound

598 Å²

Apolar buried

300 Å²

Interaction summary

HBD 3 HBA 1 HY 5 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)

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

PI · π–π interactions

No pi · π–π interactions detected for this pose.

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: strict.

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
450	1.7329626610602118	-1.22416	-26.0896	8	20	0	0.00	-	-	no	Open
404	3.2772017083554004	-1.12288	-27.0171	8	13	0	0.00	-	-	no	Open
514	3.4692528874502706	-1.06492	-26.855	5	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 -26.855kcal/mol

Ligand efficiency (LE) -1.0742kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.765

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 338.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.54

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 7.89kcal/mol

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

Docked FF energy 79.37kcal/mol

Minimised FF energy 71.48kcal/mol

SASA & burial

✓ computed

SASA (unbound) 598.1Å²

Total solvent-accessible surface area of free ligand

BSA total 389.0Å²

Buried surface area upon binding

BSA apolar 300.4Å²

Hydrophobic contacts buried

BSA polar 88.6Å²

Polar contacts buried

Fraction buried 65.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 77.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3064.8Å²

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 1480.2Å²

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