Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand OHD_Schistosoma_112

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

12.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.88, H-bond role recall 0.40

Burial

70%

Hydrophobic fit

66%

Reason: no major geometry red flags detected

1 protein-contact clashes 47% of hydrophobic surface appears solvent-exposed (7/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.355

ADMET + ECO + DL

ADMETscore (GDS)

0.345

absorption · distr. · metab.

DLscore

0.416

drug-likeness

P(SAFE)

0.06

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 (-1.201 kcal/mol/HA) ✓ Good fit quality (FQ -10.60) ✓ Good H-bonds (3 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Moderate strain (12.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-27.614

kcal/mol

-1.201

kcal/mol/HA

Fit Quality

-10.60

FQ (Leeson)

HAC

heavy atoms

412

LogP

3.17

cLogP

Final rank

1.3731

rank score

Inter norm

-1.181

normalised

Contacts

H-bonds 6

Strain ΔE

12.5 kcal/mol

SASA buried

70%

Lipo contact

66% BSA apolar/total

SASA unbound

621 Å²

Apolar buried

287 Å²

Interaction summary

HBA 3 HY 3 PI 1 CLASH 1

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	15	Native recall	0.94
Jaccard	0.88	RMSD	-
HB strict	4	Strict recall	0.33
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
34	1.3731146354112909	-1.18061	-27.6141	6	16	15	0.94	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 -27.614kcal/mol

Ligand efficiency (LE) -1.2006kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.596

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 412.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.17

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 12.49kcal/mol

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

Docked FF energy 55.45kcal/mol

Minimised FF energy 42.96kcal/mol

SASA & burial

✓ computed

SASA (unbound) 621.3Å²

Total solvent-accessible surface area of free ligand

BSA total 433.8Å²

Buried surface area upon binding

BSA apolar 286.8Å²

Hydrophobic contacts buried

BSA polar 147.0Å²

Polar contacts buried

Fraction buried 69.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 66.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2077.1Å²

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 846.8Å²

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