FAIRMol

Z46033738

Pose ID 12045 Compound 3173 Pose 524

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 Z46033738
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 medium Native strong SASA done
Strain ΔE
6.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.42
Burial
74%
Hydrophobic fit
87%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.4 kcal/mol) ✓ Excellent LE (-0.859 kcal/mol/HA) ✓ Good fit quality (FQ -7.46) ✓ Good H-bonds (4 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-18.892
kcal/mol
LE
-0.859
kcal/mol/HA
Fit Quality
-7.46
FQ (Leeson)
HAC
22
heavy atoms
MW
292
Da
LogP
3.93
cLogP
Strain ΔE
6.4 kcal/mol
SASA buried
74%
Lipo contact
87% BSA apolar/total
SASA unbound
556 Ų
Apolar buried
358 Ų

Interaction summary

HB 4 HY 23 PI 1 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.986Score-18.892
Inter norm-0.960Intra norm0.101
Top1000noExcludedno
Contacts14H-bonds4
Artifact reasongeometry warning; 7 clashes; 2 protein clashes
Residues
CYS52 GLU18 GLY13 GLY49 GLY50 ILE339 LEU17 MET113 SER109 SER14 THR335 TRP21 TYR110 VAL53

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 overlap8Native recall0.62
Jaccard0.42RMSD-
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
491 0.4708081141710543 -1.20569 -25.9726 6 15 0 0.00 - - no Open
489 2.8659796177105843 -1.33095 -31.3339 9 21 0 0.00 - - no Open
524 2.986202682502286 -0.960011 -18.8921 4 14 8 0.62 - - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -18.892kcal/mol
Ligand efficiency (LE) -0.8587kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.455
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 292.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.93
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 6.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 50.30kcal/mol
Minimised FF energy 43.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 555.7Ų
Total solvent-accessible surface area of free ligand
BSA total 409.3Ų
Buried surface area upon binding
BSA apolar 357.8Ų
Hydrophobic contacts buried
BSA polar 51.4Ų
Polar contacts buried
Fraction buried 73.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3071.8Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1481.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)