FAIRMol

NMT-TY0566

Pose ID 11172 Compound 1408 Pose 329

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-TY0566
PDB5S9T↗

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
18.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.62, H-bond role recall 1.00
Burial
85%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.136 kcal/mol/HA) ✓ Good fit quality (FQ -9.31) ✓ Good H-bonds (5 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Moderate strain (18.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.587
kcal/mol
LE
-1.136
kcal/mol/HA
Fit Quality
-9.31
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Final rank
1.8110
rank score
Inter norm
-1.178
normalised
Contacts
14
H-bonds 6
Strain ΔE
18.7 kcal/mol
SASA buried
85%
Lipo contact
73% BSA apolar/total
SASA unbound
480 Ų
Apolar buried
297 Ų

Interaction summary

HBD 4 HBA 1 HY 6 PI 2 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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 overlap10Native recall0.83
Jaccard0.62RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
312 -0.12698051497752788 -1.4099 -25.1999 5 13 0 0.00 0.00 - no Open
409 1.5618486583435398 -1.25392 -19.5039 8 16 0 0.00 0.00 - no Open
329 1.810958723850599 -1.17778 -21.5875 6 14 10 0.83 1.00 - no Current
267 3.3656450884601203 -1.63439 -30.9104 5 17 0 0.00 0.00 - no Open
265 3.3810319513898386 -1.35166 -24.7621 11 18 0 0.00 0.00 - no Open
341 3.5339212025300557 -1.51737 -27.3765 9 15 0 0.00 0.00 - no Open
382 3.8196564752012465 -1.26937 -21.4516 9 16 0 0.00 0.00 - no Open
288 4.003072569334565 -1.34735 -23.6626 10 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 -21.587kcal/mol
Ligand efficiency (LE) -1.1362kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.313
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.02
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -120.78kcal/mol
Minimised FF energy -139.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 479.9Ų
Total solvent-accessible surface area of free ligand
BSA total 409.6Ų
Buried surface area upon binding
BSA apolar 297.2Ų
Hydrophobic contacts buried
BSA polar 112.4Ų
Polar contacts buried
Fraction buried 85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6344.8Ų
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 2047.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)