FAIRMol

NMT-TY0923

Pose ID 11206 Compound 1013 Pose 363

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-TY0923
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 strong SASA done
Strain ΔE
33.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.36, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.368
ADMET + ECO + DL
ADMETscore (GDS)
0.380
absorption · distr. · metab.
DLscore
0.397
drug-likeness
P(SAFE)
0.07
GDS classification
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.856 kcal/mol/HA) ✓ Good fit quality (FQ -8.17) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (33.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-24.814
kcal/mol
LE
-0.856
kcal/mol/HA
Fit Quality
-8.17
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.70
cLogP
Final rank
4.9307
rank score
Inter norm
-0.921
normalised
Contacts
18
H-bonds 11
Strain ΔE
33.5 kcal/mol
SASA buried
80%
Lipo contact
74% BSA apolar/total
SASA unbound
674 Ų
Apolar buried
400 Ų

Interaction summary

HBD 4 HBA 2 HY 6 PI 2 CLASH 2

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

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 overlap8Native recall0.67
Jaccard0.36RMSD-
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
315 1.1613107551257762 -0.988746 -29.6316 12 16 0 0.00 0.00 - no Open
321 1.5566859020986727 -0.807286 -27.8281 8 19 0 0.00 0.00 - no Open
289 1.7875256004417812 -1.01576 -34.0347 10 17 0 0.00 0.00 - no Open
303 1.9342035494482892 -1.16396 -39.3269 9 13 0 0.00 0.00 - no Open
334 2.6091504176910982 -0.826197 -26.015 10 18 0 0.00 0.00 - no Open
367 3.0749634020371825 -0.990903 -25.5451 4 19 0 0.00 0.00 - no Open
438 3.445947979401607 -0.914081 -26.2321 6 18 0 0.00 0.00 - no Open
371 3.468473637160046 -0.952937 -25.382 5 17 0 0.00 0.00 - no Open
320 3.511127472097206 -0.833155 -22.5447 5 15 0 0.00 0.00 - no Open
407 3.597340957942763 -0.84589 -24.7448 9 14 0 0.00 0.00 - no Open
279 3.925792386612066 -1.17176 -34.1016 10 22 0 0.00 0.00 - no Open
286 4.0643906114359885 -0.970755 -26.4205 11 14 0 0.00 0.00 - no Open
307 4.098407011813724 -1.05234 -31.7217 5 14 0 0.00 0.00 - no Open
350 4.5986329465174585 -0.670614 -26.6886 7 11 0 0.00 0.00 - no Open
363 4.930702432756965 -0.921212 -24.8139 11 18 8 0.67 0.00 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.814kcal/mol
Ligand efficiency (LE) -0.8557kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.168
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.70
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -30.24kcal/mol
Minimised FF energy -63.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 674.2Ų
Total solvent-accessible surface area of free ligand
BSA total 542.7Ų
Buried surface area upon binding
BSA apolar 399.7Ų
Hydrophobic contacts buried
BSA polar 143.0Ų
Polar contacts buried
Fraction buried 80.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6519.2Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2053.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)