FAIRMol

Z56891526

Pose ID 11402 Compound 4794 Pose 559

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z56891526
PDB5S9T↗

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 medium Native mixed SASA done
Strain ΔE
25.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.33, Jaccard 0.19, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular 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 (-1.007 kcal/mol/HA) ✓ Good fit quality (FQ -8.26) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ High strain energy (25.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-19.139
kcal/mol
LE
-1.007
kcal/mol/HA
Fit Quality
-8.26
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
1.39
cLogP
Final rank
3.8014
rank score
Inter norm
-1.178
normalised
Contacts
13
H-bonds 9
Strain ΔE
25.4 kcal/mol
SASA buried
80%
Lipo contact
65% BSA apolar/total
SASA unbound
490 Ų
Apolar buried
256 Ų

Interaction summary

HBD 2 HBA 5 HY 6 PI 1 CLASH 4

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.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap4Native recall0.33
Jaccard0.19RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
551 3.1648334261698836 -1.34099 -23.6548 9 17 0 0.00 0.00 - no Open
559 3.8013867832757016 -1.17795 -19.1385 9 13 4 0.33 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 -19.139kcal/mol
Ligand efficiency (LE) -1.0073kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.256
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.39
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 82.62kcal/mol
Minimised FF energy 57.17kcal/mol

SASA & burial

✓ computed
SASA (unbound) 490.4Ų
Total solvent-accessible surface area of free ligand
BSA total 391.3Ų
Buried surface area upon binding
BSA apolar 255.6Ų
Hydrophobic contacts buried
BSA polar 135.7Ų
Polar contacts buried
Fraction buried 79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6337.6Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2063.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)