FAIRMol

Z89541367

Pose ID 13399 Compound 2223 Pose 520

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 Z89541367
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
16.8 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
55%
Hydrophobic fit
89%
Reason: 13 internal clashes
13 intramolecular clashes 55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.674 kcal/mol/HA) ✓ Good fit quality (FQ -6.29) ✓ Good H-bonds (5 bonds) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (16.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-18.191
kcal/mol
LE
-0.674
kcal/mol/HA
Fit Quality
-6.29
FQ (Leeson)
HAC
27
heavy atoms
MW
361
Da
LogP
3.22
cLogP
Final rank
3.3241
rank score
Inter norm
-0.705
normalised
Contacts
7
H-bonds 5
Strain ΔE
16.8 kcal/mol
SASA buried
55%
Lipo contact
89% BSA apolar/total
SASA unbound
643 Ų
Apolar buried
315 Ų

Interaction summary

HBD 2 HBA 3 HY 3 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.50RMSD-
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
494 0.7242754673993356 -1.13727 -28.9646 5 16 0 0.00 0.00 - no Open
500 2.9408840357454507 -1.08398 -29.6093 6 13 0 0.00 0.00 - no Open
520 3.324068012202322 -0.705259 -18.1914 5 7 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 -18.191kcal/mol
Ligand efficiency (LE) -0.6738kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.286
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 361.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.22
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 40.26kcal/mol
Minimised FF energy 23.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 643.1Ų
Total solvent-accessible surface area of free ligand
BSA total 352.1Ų
Buried surface area upon binding
BSA apolar 314.7Ų
Hydrophobic contacts buried
BSA polar 37.3Ų
Polar contacts buried
Fraction buried 54.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3109.0Ų
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 1514.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)