FAIRMol

Z19138088

Pose ID 11278 Compound 651 Pose 435

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 Z19138088
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 medium Native mixed SASA done
Strain ΔE
30.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.27, H-bond role recall 0.00
Burial
78%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
1 protein-contact clashes 36% of hydrophobic surface appears solvent-exposed (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.699 kcal/mol/HA) ✓ Good fit quality (FQ -6.99) ✓ Good H-bonds (3 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (30.5 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (19)
Score
-23.752
kcal/mol
LE
-0.699
kcal/mol/HA
Fit Quality
-6.99
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Final rank
1.9302
rank score
Inter norm
-0.728
normalised
Contacts
16
H-bonds 6
Strain ΔE
30.5 kcal/mol
SASA buried
78%
Lipo contact
76% BSA apolar/total
SASA unbound
647 Ų
Apolar buried
383 Ų

Interaction summary

HBA 3 HY 5 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap6Native recall0.50
Jaccard0.27RMSD-
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
435 1.9301717756467363 -0.72761 -23.752 6 16 6 0.50 0.00 - no Current
334 2.0263869649204853 -0.930222 -27.1777 3 21 0 0.00 0.00 - no Open
395 2.0501377984473983 -0.787007 -19.7508 5 14 0 0.00 0.00 - no Open
397 2.752858282721569 -0.800489 -23.9414 10 17 0 0.00 0.00 - no Open
396 2.7601535713818413 -0.591573 -16.9942 5 14 0 0.00 0.00 - no Open
381 2.9359635508409108 -0.793642 -19.3973 6 14 0 0.00 0.00 - no Open
450 3.1523302745872246 -0.760382 -22.134 3 18 0 0.00 0.00 - no Open
379 3.2188609293194674 -0.712407 -23.9203 8 17 0 0.00 0.00 - no Open
418 3.4321465037133247 -0.816749 -26.4904 4 18 0 0.00 0.00 - no Open
407 3.5524489581677203 -0.633858 -18.4382 7 15 0 0.00 0.00 - no Open
370 3.7807067079968997 -0.979467 -27.5375 10 15 0 0.00 0.00 - no Open
493 3.8486675627744926 -0.726729 -19.7364 7 15 0 0.00 0.00 - no Open
366 4.10912935177256 -0.834923 -27.5266 11 20 0 0.00 0.00 - no Open
336 4.160825631036783 -0.993151 -30.1156 5 15 0 0.00 0.00 - no Open
464 5.0362869852581325 -0.819442 -25.2435 6 21 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 -23.752kcal/mol
Ligand efficiency (LE) -0.6986kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.990
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.20
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 85.48kcal/mol
Minimised FF energy 54.99kcal/mol

SASA & burial

✓ computed
SASA (unbound) 647.0Ų
Total solvent-accessible surface area of free ligand
BSA total 502.2Ų
Buried surface area upon binding
BSA apolar 383.0Ų
Hydrophobic contacts buried
BSA polar 119.2Ų
Polar contacts buried
Fraction buried 77.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6468.6Ų
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 2070.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)