FAIRMol

Z49613256

Pose ID 11458 Compound 1332 Pose 615

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 Z49613256
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
47.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.25, Jaccard 0.14, H-bond role recall 0.00
Burial
69%
Hydrophobic fit
71%
Reason: strain 47.0 kcal/mol
strain ΔE 47.0 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (8/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.079 kcal/mol/HA) ✓ Good fit quality (FQ -9.67) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (47.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-25.888
kcal/mol
LE
-1.079
kcal/mol/HA
Fit Quality
-9.67
FQ (Leeson)
HAC
24
heavy atoms
MW
326
Da
LogP
2.38
cLogP
Final rank
4.0132
rank score
Inter norm
-1.016
normalised
Contacts
13
H-bonds 11
Strain ΔE
47.0 kcal/mol
SASA buried
69%
Lipo contact
71% BSA apolar/total
SASA unbound
570 Ų
Apolar buried
279 Ų

Interaction summary

HBD 2 HBA 4 HY 5 PI 1 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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 overlap3Native recall0.25
Jaccard0.14RMSD-
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
597 0.9352703103012746 -0.954539 -17.403 4 17 0 0.00 0.00 - no Open
608 2.7523442139523118 -1.14307 -25.1495 6 11 0 0.00 0.00 - no Open
615 4.013237283224836 -1.01599 -25.8883 11 13 3 0.25 0.00 - no Current
631 4.844010681220206 -1.47568 -34.2785 16 18 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 -25.888kcal/mol
Ligand efficiency (LE) -1.0787kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.667
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 326.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.38
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 47.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 191.14kcal/mol
Minimised FF energy 144.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 569.9Ų
Total solvent-accessible surface area of free ligand
BSA total 393.6Ų
Buried surface area upon binding
BSA apolar 279.4Ų
Hydrophobic contacts buried
BSA polar 114.2Ų
Polar contacts buried
Fraction buried 69.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6385.6Ų
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 2103.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)