FAIRMol

KB_chagas_202

Pose ID 13068 Compound 269 Pose 189

DB fairmolDocking 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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand KB_chagas_202
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
22.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 1.00
Burial
56%
Hydrophobic fit
94%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.648 kcal/mol/HA) ✓ Good fit quality (FQ -6.05) ✓ Good H-bonds (4 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (94%) ✗ High strain energy (22.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-17.501
kcal/mol
LE
-0.648
kcal/mol/HA
Fit Quality
-6.05
FQ (Leeson)
HAC
27
heavy atoms
MW
366
Da
LogP
0.92
cLogP
Final rank
2.6191
rank score
Inter norm
-0.700
normalised
Contacts
12
H-bonds 4
Strain ΔE
22.8 kcal/mol
SASA buried
56%
Lipo contact
94% BSA apolar/total
SASA unbound
670 Ų
Apolar buried
355 Ų

Interaction summary

HBD 2 HBA 2 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.43RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL: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:264; 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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
174 1.4218651417331085 -0.836875 -19.4836 4 10 0 0.00 0.00 - no Open
186 1.7824810351895748 -0.974766 -21.3766 3 16 0 0.00 0.00 - no Open
189 2.6191014864165867 -0.699903 -17.5012 4 12 6 0.75 1.00 - 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 -17.501kcal/mol
Ligand efficiency (LE) -0.6482kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.047
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 366.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.92
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 147.22kcal/mol
Minimised FF energy 124.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 669.7Ų
Total solvent-accessible surface area of free ligand
BSA total 377.1Ų
Buried surface area upon binding
BSA apolar 354.6Ų
Hydrophobic contacts buried
BSA polar 22.5Ų
Polar contacts buried
Fraction buried 56.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 94.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3177.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1515.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)