FAIRMol

Z19138088

Pose ID 13275 Compound 651 Pose 396

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z19138088
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry high Native strong SASA done
Strain ΔE
24.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.57, H-bond role recall 0.00
Burial
60%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
2 protein-contact clashes
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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.500 kcal/mol/HA) ✓ Good fit quality (FQ -5.00) ✓ Good H-bonds (4 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (24.4 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (22)
Score
-16.994
kcal/mol
LE
-0.500
kcal/mol/HA
Fit Quality
-5.00
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Final rank
2.7602
rank score
Inter norm
-0.592
normalised
Contacts
14
H-bonds 5
Strain ΔE
24.4 kcal/mol
SASA buried
60%
Lipo contact
73% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
304 Ų

Interaction summary

HBD 2 HBA 2 HY 3 PI 3 CLASH 2

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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.57RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A: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 0 0.00 0.00 - no Open
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 8 1.00 0.00 - no Current
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 -16.994kcal/mol
Ligand efficiency (LE) -0.4998kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.001
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) 24.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 78.95kcal/mol
Minimised FF energy 54.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.6Ų
Total solvent-accessible surface area of free ligand
BSA total 415.5Ų
Buried surface area upon binding
BSA apolar 303.5Ų
Hydrophobic contacts buried
BSA polar 112.0Ų
Polar contacts buried
Fraction buried 59.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3062.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1528.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)