FAIRMol

NMT-TY0447

Pose ID 11821 Compound 4032 Pose 300

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-TY0447
PDB6RB5↗

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 mixed SASA done
Strain ΔE
10.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.54, Jaccard 0.37
Burial
76%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.961 kcal/mol/HA) ✓ Good fit quality (FQ -8.20) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (10.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-20.190
kcal/mol
LE
-0.961
kcal/mol/HA
Fit Quality
-8.20
FQ (Leeson)
HAC
21
heavy atoms
MW
304
Da
LogP
2.00
cLogP
Final rank
1.6847
rank score
Inter norm
-1.012
normalised
Contacts
13
H-bonds 4
Strain ΔE
10.6 kcal/mol
SASA buried
76%
Lipo contact
75% BSA apolar/total
SASA unbound
551 Ų
Apolar buried
316 Ų

Interaction summary

HBD 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: 1.

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.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap7Native recall0.54
Jaccard0.37RMSD-
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
335 1.5194967487690838 -1.0163 -20.0666 4 13 7 0.54 - - no Open
300 1.6846590432116946 -1.01232 -20.1901 4 13 7 0.54 - - no Current
280 3.7752707121830755 -1.33779 -26.6408 8 16 0 0.00 - - no Open
237 3.875077357919454 -1.33963 -26.5646 8 16 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 -20.190kcal/mol
Ligand efficiency (LE) -0.9614kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.201
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 304.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.00
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -66.06kcal/mol
Minimised FF energy -76.66kcal/mol

SASA & burial

✓ computed
SASA (unbound) 550.8Ų
Total solvent-accessible surface area of free ligand
BSA total 420.9Ų
Buried surface area upon binding
BSA apolar 316.2Ų
Hydrophobic contacts buried
BSA polar 104.7Ų
Polar contacts buried
Fraction buried 76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3048.4Ų
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 1464.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)