FAIRMol

Z44848907

Pose ID 12139 Compound 1418 Pose 618

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
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z44848907
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 mixed SASA done
Strain ΔE
35.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.35
Burial
64%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.731 kcal/mol/HA) ✓ Good fit quality (FQ -7.42) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Very high strain energy (35.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-26.298
kcal/mol
LE
-0.731
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
36
heavy atoms
MW
482
Da
LogP
5.06
cLogP
Strain ΔE
35.7 kcal/mol
SASA buried
64%
Lipo contact
78% BSA apolar/total
SASA unbound
803 Ų
Apolar buried
396 Ų

Interaction summary

HB 2 HY 24 PI 2 CLASH 1

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 rank2.639Score-26.298
Inter norm-0.601Intra norm-0.130
Top1000noExcludedno
Contacts14H-bonds2
Artifact reasongeometry warning; 16 clashes; 1 protein clash; high strain Δ 35.7
Residues
CYS52 CYS57 FAD501 GLU18 ILE339 LEU17 LYS61 MET113 PRO336 SER14 THR335 TRP21 TYR110 VAL58

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
Jaccard0.35RMSD-
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
618 2.638731720341835 -0.600788 -26.298 2 14 7 0.54 - - no Current
620 2.6615284474383443 -0.620927 -20.0039 5 20 0 0.00 - - no Open
614 3.648340729911239 -0.85465 -24.416 3 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 -26.298kcal/mol
Ligand efficiency (LE) -0.7305kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.425
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 481.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.06
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 133.84kcal/mol
Minimised FF energy 98.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 802.5Ų
Total solvent-accessible surface area of free ligand
BSA total 511.4Ų
Buried surface area upon binding
BSA apolar 396.3Ų
Hydrophobic contacts buried
BSA polar 115.1Ų
Polar contacts buried
Fraction buried 63.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3258.9Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1495.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)