FAIRMol

NMT-TY0928

Pose ID 9926 Compound 307 Pose 440

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand NMT-TY0928
PDB9IFF↗

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
38.6 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.62, Jaccard 0.44
Burial
72%
Hydrophobic fit
65%
Reason: 9 internal clashes
9 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.126 kcal/mol/HA) ✓ Good fit quality (FQ -10.09) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Very high strain energy (38.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-27.022
kcal/mol
LE
-1.126
kcal/mol/HA
Fit Quality
-10.09
FQ (Leeson)
HAC
24
heavy atoms
MW
371
Da
LogP
-0.09
cLogP
Final rank
2.9671
rank score
Inter norm
-1.026
normalised
Contacts
13
H-bonds 10
Strain ΔE
38.6 kcal/mol
SASA buried
72%
Lipo contact
65% BSA apolar/total
SASA unbound
583 Ų
Apolar buried
273 Ų

Interaction summary

HBD 4 HBA 2 HY 5 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap8Native recall0.62
Jaccard0.44RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
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:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
292 1.7946739624493355 -1.19096 -30.682 8 13 0 0.00 - - no Open
391 1.924012194694617 -1.22878 -31.9908 7 16 0 0.00 - - no Open
371 2.860721822836255 -1.13963 -23.8328 6 17 0 0.00 - - no Open
440 2.967120976705636 -1.02603 -27.0223 10 13 8 0.62 - - no Current
321 3.3317421160485563 -1.00101 -23.3908 7 18 0 0.00 - - no Open
366 3.4743736314794007 -0.96628 -26.6162 10 14 0 0.00 - - no Open
337 3.529383570256196 -1.09969 -28.9223 16 14 0 0.00 - - no Open
374 3.8228138562848994 -1.15583 -29.9842 8 15 0 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 -27.022kcal/mol
Ligand efficiency (LE) -1.1259kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.090
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.09
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -18.28kcal/mol
Minimised FF energy -56.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 583.2Ų
Total solvent-accessible surface area of free ligand
BSA total 422.4Ų
Buried surface area upon binding
BSA apolar 273.2Ų
Hydrophobic contacts buried
BSA polar 149.3Ų
Polar contacts buried
Fraction buried 72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2830.2Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1517.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)