FAIRMol

NMT-TY0943

Pose ID 11215 Compound 478 Pose 372

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 NMT-TY0943
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 strong SASA done
Strain ΔE
68.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.39, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
63%
Reason: strain 68.5 kcal/mol
strain ΔE 68.5 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 41% of hydrophobic surface appears solvent-exposed (7/17 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 Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.835 kcal/mol/HA) ✓ Good fit quality (FQ -7.97) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Extreme strain energy (68.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-24.217
kcal/mol
LE
-0.835
kcal/mol/HA
Fit Quality
-7.97
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.24
cLogP
Final rank
4.7441
rank score
Inter norm
-0.828
normalised
Contacts
20
H-bonds 8
Strain ΔE
68.5 kcal/mol
SASA buried
82%
Lipo contact
63% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
332 Ų

Interaction summary

HBD 3 HBA 5 HY 4 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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
Jaccard0.39RMSD-
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
348 0.8052625623810137 -0.956826 -26.5786 1 13 0 0.00 0.00 - no Open
330 1.329263884816044 -0.859526 -24.8294 4 17 0 0.00 0.00 - no Open
326 2.453092962966273 -0.93103 -26.9955 10 12 0 0.00 0.00 - no Open
376 2.4975808499608676 -0.967058 -25.9968 4 17 0 0.00 0.00 - no Open
397 2.750322901945091 -1.0068 -27.2349 6 15 0 0.00 0.00 - no Open
286 2.8402209002504564 -1.18094 -33.1271 8 21 0 0.00 0.00 - no Open
340 3.0348573502876355 -0.845126 -25.451 13 14 0 0.00 0.00 - no Open
307 3.364737405609164 -1.16289 -34.6979 10 15 0 0.00 0.00 - no Open
383 3.6446324022786087 -0.978854 -27.1972 6 14 0 0.00 0.00 - no Open
372 4.744139486087101 -0.827695 -24.2166 8 20 9 0.75 0.00 - no Current
292 5.145683840208263 -1.07823 -23.7962 10 13 0 0.00 0.00 - no Open
299 6.264571217814828 -0.9861 -22.256 10 23 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 -24.217kcal/mol
Ligand efficiency (LE) -0.8351kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.971
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.24
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 68.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -19.95kcal/mol
Minimised FF energy -88.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.4Ų
Total solvent-accessible surface area of free ligand
BSA total 530.0Ų
Buried surface area upon binding
BSA apolar 331.7Ų
Hydrophobic contacts buried
BSA polar 198.3Ų
Polar contacts buried
Fraction buried 82.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6439.7Ų
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 2059.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)