Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T18

T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)

Ligand Z57026604

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

Likely artefact or unreliable pose

Binding strong Geometry medium Native mixed SASA done

Strain ΔE

30.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.54, Jaccard 0.39

Burial

68%

Hydrophobic fit

83%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.408

ADMET + ECO + DL

ADMETscore (GDS)

0.431

absorption · distr. · metab.

DLscore

0.442

drug-likeness

P(SAFE)

0.44

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.977 kcal/mol/HA) ✓ Good fit quality (FQ -8.88) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Very high strain energy (30.3 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (10)

Score

-24.430

kcal/mol

-0.977

kcal/mol/HA

Fit Quality

-8.88

FQ (Leeson)

HAC

heavy atoms

350

LogP

4.40

cLogP

Final rank

1.1626

rank score

Inter norm

-0.876

normalised

Contacts

H-bonds 4

Strain ΔE

30.3 kcal/mol

SASA buried

68%

Lipo contact

83% BSA apolar/total

SASA unbound

628 Å²

Apolar buried

355 Å²

Interaction summary

HBA 2 HY 7 PI 2 CLASH 3

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	13
Pose	Open native pose	HB	0
IFP residues	ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap	7	Native recall	0.54
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	T18	Atoms	7550
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
466	1.162572639156309	-0.876306	-24.4296	4	12	7	0.54	-	-	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 -24.430kcal/mol

Ligand efficiency (LE) -0.9772kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.883

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 350.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.40

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 30.28kcal/mol

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

Docked FF energy 104.14kcal/mol

Minimised FF energy 73.86kcal/mol

SASA & burial

✓ computed

SASA (unbound) 628.1Å²

Total solvent-accessible surface area of free ligand

BSA total 427.0Å²

Buried surface area upon binding

BSA apolar 355.4Å²

Hydrophobic contacts buried

BSA polar 71.6Å²

Polar contacts buried

Fraction buried 68.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 83.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3145.4Å²

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 1468.4Å²

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