FAIRMol

NMT-TY0622

Pose ID 11190 Compound 524 Pose 347

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-TY0622
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 high Native strong SASA done
Strain ΔE
28.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.41, H-bond role recall 0.00
Burial
84%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.768
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.581
ADMET + ECO + DL
ADMETscore (GDS)
0.597
absorption · distr. · metab.
DLscore
0.440
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 (-1.060 kcal/mol/HA) ✓ Good fit quality (FQ -9.64) ✓ Good H-bonds (5 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (28.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-26.504
kcal/mol
LE
-1.060
kcal/mol/HA
Fit Quality
-9.64
FQ (Leeson)
HAC
25
heavy atoms
MW
381
Da
LogP
2.01
cLogP
Final rank
3.9186
rank score
Inter norm
-1.054
normalised
Contacts
19
H-bonds 6
Strain ΔE
28.9 kcal/mol
SASA buried
84%
Lipo contact
71% BSA apolar/total
SASA unbound
595 Ų
Apolar buried
354 Ų

Interaction summary

HBD 3 HBA 2 HY 7 PI 0 CLASH 1

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

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.41RMSD-
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
308 0.3842150656616825 -0.951549 -25.0395 4 17 0 0.00 0.00 - no Open
276 1.2600618081157402 -1.12204 -28.7499 9 15 0 0.00 0.00 - no Open
288 1.7018393222780244 -1.13668 -28.6792 9 14 0 0.00 0.00 - no Open
352 1.9271195694416656 -1.10716 -29.8519 6 13 0 0.00 0.00 - no Open
341 1.927730112535267 -0.859185 -22.1976 9 12 0 0.00 0.00 - no Open
273 1.9961552376915304 -1.35584 -31.5197 14 17 0 0.00 0.00 - no Open
327 2.0961391154894002 -0.86609 -19.9983 5 13 0 0.00 0.00 - no Open
392 2.3248094781583672 -0.940735 -21.0428 11 16 0 0.00 0.00 - no Open
308 2.8353655663354234 -1.13363 -28.9578 5 19 0 0.00 0.00 - no Open
378 2.966730885309019 -1.23963 -28.1056 8 15 0 0.00 0.00 - no Open
423 3.5162080347453757 -1.16596 -29.4186 9 16 0 0.00 0.00 - no Open
361 3.58426702200673 -1.22019 -28.4754 6 15 0 0.00 0.00 - no Open
268 3.6431928517433407 -1.15199 -28.179 10 14 0 0.00 0.00 - no Open
327 3.7246234846293826 -1.02174 -24.8257 12 17 0 0.00 0.00 - no Open
347 3.9186485478235458 -1.05383 -26.5042 6 19 9 0.75 0.00 - no Current
269 4.208957465627367 -1.25064 -26.887 9 18 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 -26.504kcal/mol
Ligand efficiency (LE) -1.0602kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.638
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 381.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.01
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -66.60kcal/mol
Minimised FF energy -95.47kcal/mol

SASA & burial

✓ computed
SASA (unbound) 594.9Ų
Total solvent-accessible surface area of free ligand
BSA total 498.1Ų
Buried surface area upon binding
BSA apolar 353.8Ų
Hydrophobic contacts buried
BSA polar 144.3Ų
Polar contacts buried
Fraction buried 83.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6430.9Ų
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 2046.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)