FAIRMol

Z24181579

Pose ID 11449 Compound 1273 Pose 606

DB SELECTIONDocking 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 Z24181579
PDB5S9T↗

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 but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
19.4 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.67, Jaccard 0.38, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
76%
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.807 kcal/mol/HA) ✓ Good fit quality (FQ -8.01) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (19.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-26.630
kcal/mol
LE
-0.807
kcal/mol/HA
Fit Quality
-8.01
FQ (Leeson)
HAC
33
heavy atoms
MW
467
Da
LogP
3.11
cLogP
Strain ΔE
19.4 kcal/mol
SASA buried
82%
Lipo contact
76% BSA apolar/total
SASA unbound
746 Ų
Apolar buried
467 Ų

Interaction summary

HB 4 HY 17 PI 3 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank2.039Score-26.630
Inter norm-0.784Intra norm-0.023
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 9 clashes; 1 protein clash
Residues
ARG228 ARG361 CYS375 GLY196 GLY197 GLY376 ILE285 LEU227 LEU332 LEU334 PHE198 PHE230 SER364 THR374 TYR221 VAL362 VAL366

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
Jaccard0.38RMSD-
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
606 2.0387116795349516 -0.783773 -26.6302 4 17 8 0.67 0.00 - no Current
594 2.280406481965539 -0.963317 -29.9961 4 15 0 0.00 0.00 - no Open
593 4.016783419434528 -0.82401 -26.1742 12 16 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 -26.630kcal/mol
Ligand efficiency (LE) -0.8070kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.007
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.11
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 56.91kcal/mol
Minimised FF energy 37.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 746.3Ų
Total solvent-accessible surface area of free ligand
BSA total 614.7Ų
Buried surface area upon binding
BSA apolar 467.4Ų
Hydrophobic contacts buried
BSA polar 147.3Ų
Polar contacts buried
Fraction buried 82.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6585.0Ų
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 2069.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)