FAIRMol

Z19081445

Pose ID 7898 Compound 2349 Pose 446

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
T12
T. brucei R5P T. brucei
Ligand Z19081445
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 medium Native strong SASA done
Strain ΔE
17.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.74, H-bond role recall 0.50
Burial
74%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (8/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.052 kcal/mol/HA) ✓ Good fit quality (FQ -9.82) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Moderate strain (17.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-28.416
kcal/mol
LE
-1.052
kcal/mol/HA
Fit Quality
-9.82
FQ (Leeson)
HAC
27
heavy atoms
MW
409
Da
LogP
1.78
cLogP
Final rank
2.9414
rank score
Inter norm
-1.068
normalised
Contacts
17
H-bonds 11
Strain ΔE
17.6 kcal/mol
SASA buried
74%
Lipo contact
63% BSA apolar/total
SASA unbound
648 Ų
Apolar buried
302 Ų

Interaction summary

HBA 8 HY 4 PI 2 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
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
Jaccard0.74RMSD-
HB strict7Strict recall0.58
HB same residue+role5HB role recall0.50
HB same residue5HB residue recall0.50

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
439 0.0743856335420149 -0.834733 -24.5557 2 18 0 0.00 0.00 - no Open
452 2.0757484440128646 -0.945836 -25.3647 11 17 5 0.31 0.20 - no Open
446 2.9414058320002976 -1.06804 -28.416 11 17 14 0.88 0.50 - 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 -28.416kcal/mol
Ligand efficiency (LE) -1.0524kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.819
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.78
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 3.46kcal/mol
Minimised FF energy -14.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 647.9Ų
Total solvent-accessible surface area of free ligand
BSA total 479.0Ų
Buried surface area upon binding
BSA apolar 302.5Ų
Hydrophobic contacts buried
BSA polar 176.6Ų
Polar contacts buried
Fraction buried 73.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2096.5Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 814.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)