FAIRMol

KB_chagas_104

Pose ID 7564 Compound 3309 Pose 112

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T12
T. brucei R5P T. brucei
Ligand KB_chagas_104
PDB6FXS↗

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 strong SASA done
Strain ΔE
41.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.78, H-bond role recall 0.40
Burial
69%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model
ECOscore
0.359
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.485
ADMET + ECO + DL
ADMETscore (GDS)
0.569
absorption · distr. · metab.
DLscore
0.413
drug-likeness
P(SAFE)
0.76
GDS classification
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.018 kcal/mol/HA) ✓ Good fit quality (FQ -10.27) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (41.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-35.638
kcal/mol
LE
-1.018
kcal/mol/HA
Fit Quality
-10.27
FQ (Leeson)
HAC
35
heavy atoms
MW
490
Da
LogP
2.72
cLogP
Final rank
5.7613
rank score
Inter norm
-1.050
normalised
Contacts
16
H-bonds 14
Strain ΔE
41.1 kcal/mol
SASA buried
69%
Lipo contact
80% BSA apolar/total
SASA unbound
761 Ų
Apolar buried
424 Ų

Interaction summary

HBA 11 HY 3 PI 7 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap14Native recall0.88
Jaccard0.78RMSD-
HB strict6Strict recall0.50
HB same residue+role4HB role recall0.40
HB same residue4HB residue recall0.40

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG: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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
135 2.873105287369656 -0.749158 -23.1682 5 13 0 0.00 0.00 - no Open
93 3.613209796741848 -0.724488 -23.198 12 17 5 0.31 0.20 - no Open
112 5.761302332405041 -1.04951 -35.638 14 16 14 0.88 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 -35.638kcal/mol
Ligand efficiency (LE) -1.0182kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.270
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 489.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.72
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 119.92kcal/mol
Minimised FF energy 78.83kcal/mol

SASA & burial

✓ computed
SASA (unbound) 760.7Ų
Total solvent-accessible surface area of free ligand
BSA total 527.3Ų
Buried surface area upon binding
BSA apolar 423.8Ų
Hydrophobic contacts buried
BSA polar 103.6Ų
Polar contacts buried
Fraction buried 69.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2276.2Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 781.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)