FAIRMol

Z44856621

Pose ID 11319 Compound 2743 Pose 476

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 Z44856621
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
37.8 kcal/mol
Protein clashes
3
Internal clashes
7
Native overlap
contact recall 0.75, Jaccard 0.38, H-bond role recall 1.00
Burial
83%
Hydrophobic fit
77%
Reason: 7 internal clashes
3 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.729 kcal/mol/HA) ✓ Good fit quality (FQ -7.30) ✓ Good H-bonds (4 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (37.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-24.795
kcal/mol
LE
-0.729
kcal/mol/HA
Fit Quality
-7.30
FQ (Leeson)
HAC
34
heavy atoms
MW
534
Da
LogP
5.11
cLogP
Final rank
3.2078
rank score
Inter norm
-0.828
normalised
Contacts
21
H-bonds 9
Strain ΔE
37.8 kcal/mol
SASA buried
83%
Lipo contact
77% BSA apolar/total
SASA unbound
764 Ų
Apolar buried
486 Ų

Interaction summary

HBD 1 HBA 3 HY 10 PI 3 CLASH 7

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 overlap9Native recall0.75
Jaccard0.38RMSD-
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
407 0.4460464701571234 -0.902398 -26.5386 2 18 0 0.00 0.00 - no Open
441 2.134597253516552 -0.571051 -15.873 3 11 0 0.00 0.00 - no Open
476 3.207803087429654 -0.828298 -24.7951 9 21 9 0.75 1.00 - no Current
520 3.4286161390837204 -0.715677 -26.832 8 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 -24.795kcal/mol
Ligand efficiency (LE) -0.7293kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.297
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 534.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.11
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 93.25kcal/mol
Minimised FF energy 55.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 764.1Ų
Total solvent-accessible surface area of free ligand
BSA total 633.1Ų
Buried surface area upon binding
BSA apolar 485.7Ų
Hydrophobic contacts buried
BSA polar 147.3Ų
Polar contacts buried
Fraction buried 82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6596.9Ų
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 2053.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)