Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand Z26407930

PDB6FXS↗

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 strong SASA done

Strain ΔE

18.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.75, Jaccard 0.63, H-bond role recall 0.40

Burial

77%

Hydrophobic fit

68%

Reason: no major geometry red flags detected

2 protein-contact clashes

EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.395

ADMET + ECO + DL

ADMETscore (GDS)

0.409

absorption · distr. · metab.

DLscore

0.437

drug-likeness

P(SAFE)

0.63

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 (-2.042 kcal/mol/HA) ✓ Good fit quality (FQ -17.42) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (18.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-42.880

kcal/mol

-2.042

kcal/mol/HA

Fit Quality

-17.42

FQ (Leeson)

HAC

heavy atoms

316

LogP

3.83

cLogP

Final rank

2.4377

rank score

Inter norm

-1.285

normalised

Contacts

H-bonds 10

Strain ΔE

18.1 kcal/mol

SASA buried

77%

Lipo contact

68% BSA apolar/total

SASA unbound

551 Å²

Apolar buried

287 Å²

Interaction summary

HBA 7 HY 4 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)

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

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	6FXS	Contacts	16
Pose	Open native pose	HB	0
IFP residues	ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap	12	Native recall	0.75
Jaccard	0.63	RMSD	-
HB strict	6	Strict recall	0.50
HB same residue+role	4	HB role recall	0.40
HB same residue	5	HB residue recall	0.50

Protein summary

302 residues

Protein target	T12	Atoms	4598
Residues	302	Chains	2
Residue summary	ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
666	2.437685782310435	-1.28526	-42.88	10	15	12	0.75	0.40	-	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 -42.880kcal/mol

Ligand efficiency (LE) -2.0419kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -17.417

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 316.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.83

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 18.07kcal/mol

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

Docked FF energy 64.08kcal/mol

Minimised FF energy 46.02kcal/mol

SASA & burial

✓ computed

SASA (unbound) 550.6Å²

Total solvent-accessible surface area of free ligand

BSA total 422.3Å²

Buried surface area upon binding

BSA apolar 286.6Å²

Hydrophobic contacts buried

BSA polar 135.7Å²

Polar contacts buried

Fraction buried 76.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 67.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2085.2Å²

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 2454.8Å²

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

Complex non-polar SASA 758.8Å²

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