FAIRMol

NMT-TY0432

Pose ID 11165 Compound 2546 Pose 322

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 NMT-TY0432
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
54.4 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.33, Jaccard 0.18, H-bond role recall 0.00
Burial
68%
Hydrophobic fit
70%
Reason: 12 internal clashes, strain 54.4 kcal/mol
strain ΔE 54.4 kcal/mol 12 intramolecular clashes
EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model
ECOscore
0.768
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.613
ADMET + ECO + DL
ADMETscore (GDS)
0.654
absorption · distr. · metab.
DLscore
0.450
drug-likeness
P(SAFE)
0.83
GDS classification
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.515 kcal/mol/HA) ✓ Good fit quality (FQ -4.87) ✓ Good H-bonds (4 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Extreme strain energy (54.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-14.433
kcal/mol
LE
-0.515
kcal/mol/HA
Fit Quality
-4.87
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
3.33
cLogP
Final rank
2.2845
rank score
Inter norm
-0.837
normalised
Contacts
14
H-bonds 8
Strain ΔE
54.4 kcal/mol
SASA buried
68%
Lipo contact
70% BSA apolar/total
SASA unbound
666 Ų
Apolar buried
315 Ų

Interaction summary

HBD 1 HBA 3 HY 6 PI 1 CLASH 0

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
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.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap4Native recall0.33
Jaccard0.18RMSD-
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
276 1.4370460415681932 -0.857202 -20.8428 4 16 0 0.00 0.00 - no Open
279 1.5440426723862828 -0.915782 -15.5774 3 17 0 0.00 0.00 - no Open
322 2.2845055573682136 -0.837043 -14.4333 8 14 4 0.33 0.00 - no Current
328 3.9600681558418565 -0.700868 -19.9524 4 10 0 0.00 0.00 - no Open
234 4.402454043048613 -1.3024 -32.5083 11 24 0 0.00 0.00 - no Open
243 4.556144867088151 -1.00584 -21.4104 12 16 0 0.00 0.00 - no Open
264 4.751862308706498 -1.26026 -34.8667 11 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 -14.433kcal/mol
Ligand efficiency (LE) -0.5155kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.866
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.33
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 54.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -148.33kcal/mol
Minimised FF energy -202.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 666.3Ų
Total solvent-accessible surface area of free ligand
BSA total 451.2Ų
Buried surface area upon binding
BSA apolar 315.3Ų
Hydrophobic contacts buried
BSA polar 135.9Ų
Polar contacts buried
Fraction buried 67.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6466.5Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2113.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)