FAIRMol

Z55699642

Pose ID 13418 Compound 5192 Pose 539

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 Z55699642
PDB9IFH↗

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 but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
11.9 kcal/mol
Protein clashes
2
Internal clashes
9
Native overlap
contact recall 0.62, Jaccard 0.36, H-bond role recall 0.00
Burial
67%
Hydrophobic fit
83%
Reason: 9 internal clashes
2 protein-contact clashes 9 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.783 kcal/mol/HA) ✓ Good fit quality (FQ -6.91) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (11.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (9)
Score
-18.000
kcal/mol
LE
-0.783
kcal/mol/HA
Fit Quality
-6.91
FQ (Leeson)
HAC
23
heavy atoms
MW
299
Da
LogP
3.34
cLogP
Final rank
0.6614
rank score
Inter norm
-0.829
normalised
Contacts
11
H-bonds 4
Strain ΔE
11.9 kcal/mol
SASA buried
67%
Lipo contact
83% BSA apolar/total
SASA unbound
535 Ų
Apolar buried
296 Ų

Interaction summary

HBD 1 HBA 1 HY 4 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.36RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
539 0.661439625622654 -0.82932 -17.9995 4 11 5 0.62 0.00 - 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 -18.000kcal/mol
Ligand efficiency (LE) -0.7826kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.907
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 299.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.34
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 163.73kcal/mol
Minimised FF energy 151.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 534.7Ų
Total solvent-accessible surface area of free ligand
BSA total 358.9Ų
Buried surface area upon binding
BSA apolar 296.3Ų
Hydrophobic contacts buried
BSA polar 62.5Ų
Polar contacts buried
Fraction buried 67.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3023.1Ų
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 1492.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)