FAIRMol

NMT-TY0572

Pose ID 11827 Compound 3764 Pose 306

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand NMT-TY0572
PDB6RB5↗

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
30.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.40
Burial
67%
Hydrophobic fit
60%
Reason: no major geometry red flags detected
1 protein-contact 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.805 kcal/mol/HA) ✓ Good fit quality (FQ -7.32) ✓ Good H-bonds (4 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (60%) ✗ Very high strain energy (30.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-20.120
kcal/mol
LE
-0.805
kcal/mol/HA
Fit Quality
-7.32
FQ (Leeson)
HAC
25
heavy atoms
MW
367
Da
LogP
-0.59
cLogP
Final rank
4.1678
rank score
Inter norm
-1.010
normalised
Contacts
15
H-bonds 10
Strain ΔE
30.3 kcal/mol
SASA buried
67%
Lipo contact
60% BSA apolar/total
SASA unbound
617 Ų
Apolar buried
248 Ų

Interaction summary

HBD 3 HBA 1 PC 1 HY 7 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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: permissive.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap8Native recall0.62
Jaccard0.40RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
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:276; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 3.145166119669908 -1.05074 -23.6434 7 19 0 0.00 - - no Open
306 4.167779747875476 -1.01007 -20.1198 10 15 8 0.62 - - no Current
254 4.667470670593299 -1.10314 -26.2765 11 18 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 -20.120kcal/mol
Ligand efficiency (LE) -0.8048kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.316
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.59
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -90.86kcal/mol
Minimised FF energy -121.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 617.4Ų
Total solvent-accessible surface area of free ligand
BSA total 410.9Ų
Buried surface area upon binding
BSA apolar 247.6Ų
Hydrophobic contacts buried
BSA polar 163.3Ų
Polar contacts buried
Fraction buried 66.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 60.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3014.4Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1473.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)