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 Z27695369

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 high Native mixed SASA done

Strain ΔE

14.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.33, Jaccard 0.20

Burial

72%

Hydrophobic fit

85%

Reason: no major geometry red flags detected

1 protein-contact clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.367

ADMET + ECO + DL

ADMETscore (GDS)

0.343

absorption · distr. · metab.

DLscore

0.461

drug-likeness

P(SAFE)

0.37

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.809 kcal/mol/HA) ✓ Good fit quality (FQ -7.36) ✓ Good H-bonds (5 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (14.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-20.237

kcal/mol

-0.809

kcal/mol/HA

Fit Quality

-7.36

FQ (Leeson)

HAC

heavy atoms

336

LogP

3.54

cLogP

Final rank

1.8173

rank score

Inter norm

-0.921

normalised

Contacts

H-bonds 6

Strain ΔE

14.0 kcal/mol

SASA buried

72%

Lipo contact

85% BSA apolar/total

SASA unbound

630 Å²

Apolar buried

384 Å²

Interaction summary

HBD 2 HBA 3 HY 6 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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	4	Native recall	0.33
Jaccard	0.20	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
534	1.817333416945577	-0.921142	-20.2373	6	12	4	0.33	-	-	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 -20.237kcal/mol

Ligand efficiency (LE) -0.8095kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.359

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 336.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.54

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 14.03kcal/mol

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

Docked FF energy 8.25kcal/mol

Minimised FF energy -5.78kcal/mol

SASA & burial

✓ computed

SASA (unbound) 629.5Å²

Total solvent-accessible surface area of free ligand

BSA total 452.7Å²

Buried surface area upon binding

BSA apolar 383.6Å²

Hydrophobic contacts buried

BSA polar 69.1Å²

Polar contacts buried

Fraction buried 71.9%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 84.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3122.9Å²

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 1495.5Å²

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