FAIRMol

Z49638306

Pose ID 11308 Compound 3538 Pose 465

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 Z49638306
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
26.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.36, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.812 kcal/mol/HA) ✓ Good fit quality (FQ -7.84) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (26.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-24.375
kcal/mol
LE
-0.812
kcal/mol/HA
Fit Quality
-7.84
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
4.44
cLogP
Final rank
4.0044
rank score
Inter norm
-0.800
normalised
Contacts
18
H-bonds 4
Strain ΔE
26.7 kcal/mol
SASA buried
82%
Lipo contact
82% BSA apolar/total
SASA unbound
664 Ų
Apolar buried
445 Ų

Interaction summary

HBD 1 HBA 3 HY 6 PI 2 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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 overlap8Native recall0.67
Jaccard0.36RMSD-
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
383 1.2287636357355942 -1.0501 -37.6676 7 20 0 0.00 0.00 - no Open
420 1.5304501302166158 -0.780324 -26.3523 4 13 0 0.00 0.00 - no Open
436 2.785856035332341 -0.980801 -34.63 7 16 0 0.00 0.00 - no Open
497 2.955093255524448 -0.865923 -27.6702 5 14 0 0.00 0.00 - no Open
509 3.2491331708059237 -0.794232 -23.4452 7 11 0 0.00 0.00 - no Open
465 4.004368900998721 -0.799974 -24.3755 4 18 8 0.67 0.00 - no Current
391 4.4407993593659 -1.07037 -31.267 12 18 0 0.00 0.00 - no Open
426 4.8004481778310115 -0.756591 -25.3759 10 12 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.375kcal/mol
Ligand efficiency (LE) -0.8125kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.838
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.44
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 122.48kcal/mol
Minimised FF energy 95.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 664.0Ų
Total solvent-accessible surface area of free ligand
BSA total 544.1Ų
Buried surface area upon binding
BSA apolar 444.5Ų
Hydrophobic contacts buried
BSA polar 99.5Ų
Polar contacts buried
Fraction buried 81.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6523.5Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2073.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)