FAIRMol

Z295463994

Pose ID 11330 Compound 4773 Pose 487

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 Z295463994
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 high Native strong SASA done
Strain ΔE
16.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.26, H-bond role recall 1.00
Burial
79%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
1 protein-contact clashes 37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.711 kcal/mol/HA) ✓ Good fit quality (FQ -6.46) ✓ Good H-bonds (3 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (16.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-17.768
kcal/mol
LE
-0.711
kcal/mol/HA
Fit Quality
-6.46
FQ (Leeson)
HAC
25
heavy atoms
MW
333
Da
LogP
3.37
cLogP
Final rank
2.8955
rank score
Inter norm
-0.901
normalised
Contacts
12
H-bonds 5
Strain ΔE
16.3 kcal/mol
SASA buried
79%
Lipo contact
84% BSA apolar/total
SASA unbound
564 Ų
Apolar buried
374 Ų

Interaction summary

HBA 3 HY 5 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap5Native recall0.42
Jaccard0.26RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
487 2.895463873447057 -0.900664 -17.7678 5 12 5 0.42 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 -17.768kcal/mol
Ligand efficiency (LE) -0.7107kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.461
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.37
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 86.69kcal/mol
Minimised FF energy 70.37kcal/mol

SASA & burial

✓ computed
SASA (unbound) 563.9Ų
Total solvent-accessible surface area of free ligand
BSA total 444.7Ų
Buried surface area upon binding
BSA apolar 374.2Ų
Hydrophobic contacts buried
BSA polar 70.6Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6456.6Ų
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 2093.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)