FAIRMol

NMT-TY0621

Pose ID 11189 Compound 518 Pose 346

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-TY0621
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
32.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
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 (-0.875 kcal/mol/HA) ✓ Good fit quality (FQ -8.35) ✓ Good H-bonds (4 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (32.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-25.374
kcal/mol
LE
-0.875
kcal/mol/HA
Fit Quality
-8.35
FQ (Leeson)
HAC
29
heavy atoms
MW
438
Da
LogP
2.78
cLogP
Final rank
3.7743
rank score
Inter norm
-0.840
normalised
Contacts
18
H-bonds 9
Strain ΔE
32.9 kcal/mol
SASA buried
81%
Lipo contact
68% BSA apolar/total
SASA unbound
680 Ų
Apolar buried
373 Ų

Interaction summary

HBD 2 HBA 2 HY 5 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.43RMSD-
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
321 0.4312888916095546 -0.855947 -25.5191 1 14 0 0.00 0.00 - no Open
307 1.303464687200235 -0.78987 -18.3238 4 19 0 0.00 0.00 - no Open
289 1.76930837462521 -1.29932 -35.9638 10 15 0 0.00 0.00 - no Open
422 2.7545848910139727 -0.868419 -24.2502 5 17 0 0.00 0.00 - no Open
295 2.796755929845018 -1.11058 -31.8963 15 21 0 0.00 0.00 - no Open
377 2.9388887475161027 -0.975895 -27.6065 6 15 0 0.00 0.00 - no Open
360 3.268268659000955 -0.926537 -24.8747 6 16 0 0.00 0.00 - no Open
346 3.7743481783884123 -0.840004 -25.3743 9 18 9 0.75 0.00 - no Current
267 4.280322512603641 -0.963547 -25.3705 10 15 0 0.00 0.00 - no Open
326 4.289068608505349 -0.759293 -21.2289 7 14 0 0.00 0.00 - no Open
340 4.374513372828821 -0.659938 -21.0777 6 12 0 0.00 0.00 - no Open
268 4.513993838828387 -1.00962 -28.398 9 17 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 -25.374kcal/mol
Ligand efficiency (LE) -0.8750kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.352
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 437.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -83.83kcal/mol
Minimised FF energy -116.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 679.6Ų
Total solvent-accessible surface area of free ligand
BSA total 549.7Ų
Buried surface area upon binding
BSA apolar 372.6Ų
Hydrophobic contacts buried
BSA polar 177.1Ų
Polar contacts buried
Fraction buried 80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6489.2Ų
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 2062.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)