FAIRMol

NMT-TY0409

Pose ID 9886 Compound 570 Pose 400

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand NMT-TY0409
PDB9IFF↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
19.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
84%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
2 protein-contact clashes 40% of hydrophobic surface appears solvent-exposed (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.296 kcal/mol/HA) ✓ Good fit quality (FQ -10.85) ✓ Good H-bonds (4 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Moderate strain (19.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.923
kcal/mol
LE
-1.296
kcal/mol/HA
Fit Quality
-10.85
FQ (Leeson)
HAC
20
heavy atoms
MW
313
Da
LogP
0.81
cLogP
Final rank
2.4200
rank score
Inter norm
-1.290
normalised
Contacts
16
H-bonds 9
Strain ΔE
19.6 kcal/mol
SASA buried
84%
Lipo contact
63% BSA apolar/total
SASA unbound
498 Ų
Apolar buried
262 Ų

Interaction summary

HBD 3 HBA 1 HY 8 PI 1 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.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap10Native recall0.77
Jaccard0.53RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
256 0.15772456433515986 -1.39322 -27.5062 8 14 0 0.00 - - no Open
326 1.7660606604934106 -1.01819 -19.6306 9 8 0 0.00 - - no Open
277 1.8546395330541607 -1.1627 -22.7243 10 17 0 0.00 - - no Open
335 1.9539662524601658 -1.4959 -28.3343 10 14 0 0.00 - - no Open
298 2.257908716162415 -1.0958 -22.0596 7 11 0 0.00 - - no Open
400 2.419978712999776 -1.28962 -25.9234 9 16 10 0.77 - - no Current
274 2.725557170482087 -1.20833 -23.6186 8 14 0 0.00 - - no Open
372 2.95166993836523 -1.43344 -26.7737 8 13 0 0.00 - - no Open
256 3.0930541913905487 -1.30737 -26.3803 9 14 0 0.00 - - no Open
336 3.114127828859795 -1.30283 -25.5336 6 15 0 0.00 - - no Open
348 3.3534428929750644 -1.35737 -25.171 6 15 0 0.00 - - no Open
320 3.4590025533125908 -1.2212 -24.8485 8 17 0 0.00 - - no Open
230 3.7784047479922487 -1.38875 -26.8164 11 13 0 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 -25.923kcal/mol
Ligand efficiency (LE) -1.2962kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.847
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.81
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -82.93kcal/mol
Minimised FF energy -102.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 497.5Ų
Total solvent-accessible surface area of free ligand
BSA total 416.9Ų
Buried surface area upon binding
BSA apolar 262.3Ų
Hydrophobic contacts buried
BSA polar 154.6Ų
Polar contacts buried
Fraction buried 83.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2789.9Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1508.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)