FAIRMol

NMT-TY0645

Pose ID 11195 Compound 2221 Pose 352

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-TY0645
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
110.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.28, H-bond role recall 0.00
Burial
74%
Hydrophobic fit
56%
Reason: strain 110.4 kcal/mol
strain ΔE 110.4 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
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 Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.617 kcal/mol/HA) ✓ Good fit quality (FQ -6.18) ✓ Good H-bonds (5 bonds) ✓ Deep burial (74% SASA buried) ✗ Extreme strain energy (110.4 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (10) ✗ Many internal clashes (14)
Score
-20.992
kcal/mol
LE
-0.617
kcal/mol/HA
Fit Quality
-6.18
FQ (Leeson)
HAC
34
heavy atoms
MW
512
Da
LogP
0.84
cLogP
Final rank
2.6591
rank score
Inter norm
-0.663
normalised
Contacts
20
H-bonds 12
Strain ΔE
110.4 kcal/mol
SASA buried
74%
Lipo contact
56% BSA apolar/total
SASA unbound
718 Ų
Apolar buried
299 Ų

Interaction summary

HBD 5 HY 4 PI 1 CLASH 3

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 overlap7Native recall0.58
Jaccard0.28RMSD-
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
352 2.6591088902554145 -0.663334 -20.9923 12 20 7 0.58 0.00 - no Current
294 2.8169198974226206 -0.763427 -26.2094 9 19 0 0.00 0.00 - no Open
279 2.9386173620887566 -0.824993 -29.3038 8 17 0 0.00 0.00 - no Open
276 3.5602412451860346 -0.921957 -25.3809 11 22 0 0.00 0.00 - no Open
397 4.2664490731645195 -0.737645 -24.1163 16 16 0 0.00 0.00 - no Open
258 5.655842000188189 -0.696138 -14.4763 16 16 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 -20.992kcal/mol
Ligand efficiency (LE) -0.6174kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.178
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 512.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.84
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 110.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -79.69kcal/mol
Minimised FF energy -190.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 718.2Ų
Total solvent-accessible surface area of free ligand
BSA total 535.4Ų
Buried surface area upon binding
BSA apolar 298.6Ų
Hydrophobic contacts buried
BSA polar 236.7Ų
Polar contacts buried
Fraction buried 74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 55.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6402.4Ų
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 2069.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)