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 ulfkktlib_1310

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 strong SASA done

Strain ΔE

8.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.58, Jaccard 0.39

Burial

80%

Hydrophobic fit

83%

Reason: no major geometry red flags detected

4 protein-contact clashes 4 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.983 kcal/mol/HA) ✓ Good fit quality (FQ -8.68) ✓ Good H-bonds (3 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (8.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-22.608

kcal/mol

-0.983

kcal/mol/HA

Fit Quality

-8.68

FQ (Leeson)

HAC

heavy atoms

308

LogP

1.95

cLogP

Final rank

1.9944

rank score

Inter norm

-1.005

normalised

Contacts

H-bonds 6

Strain ΔE

8.6 kcal/mol

SASA buried

80%

Lipo contact

83% BSA apolar/total

SASA unbound

562 Å²

Apolar buried

372 Å²

Interaction summary

HBD 2 HBA 1 HY 9 PI 1 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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	7	Native recall	0.58
Jaccard	0.39	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
309	1.9944308171706764	-1.00507	-22.6075	6	13	7	0.58	-	-	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 -22.608kcal/mol

Ligand efficiency (LE) -0.9829kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.675

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 308.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.95

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 8.62kcal/mol

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

Docked FF energy 84.48kcal/mol

Minimised FF energy 75.86kcal/mol

SASA & burial

✓ computed

SASA (unbound) 561.7Å²

Total solvent-accessible surface area of free ligand

BSA total 446.9Å²

Buried surface area upon binding

BSA apolar 371.7Å²

Hydrophobic contacts buried

BSA polar 75.2Å²

Polar contacts buried

Fraction buried 79.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 83.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3111.6Å²

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 4076.6Å²

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

Complex non-polar SASA 1443.6Å²

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