FAIRMol

Z20024774

Pose ID 11948 Compound 1221 Pose 427

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 Z20024774
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
31.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.61
Burial
69%
Hydrophobic fit
82%
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 (-0.673 kcal/mol/HA) ✓ Good fit quality (FQ -6.73) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (31.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (7)
Score
-22.875
kcal/mol
LE
-0.673
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
34
heavy atoms
MW
479
Da
LogP
3.73
cLogP
Strain ΔE
31.4 kcal/mol
SASA buried
69%
Lipo contact
82% BSA apolar/total
SASA unbound
771 Ų
Apolar buried
433 Ų

Interaction summary

HB 2 HY 23 PI 3 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 rank0.585Score-22.875
Inter norm-0.623Intra norm-0.050
Top1000noExcludedno
Contacts16H-bonds2
Artifact reasongeometry warning; 7 clashes; 2 protein contact clashes; moderate strain Δ 28.2
Residues
ASP116 CYS52 GLU18 GLY112 GLY13 GLY49 ILE106 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 overlap11Native recall0.85
Jaccard0.61RMSD-
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
427 0.5851714045603333 -0.622543 -22.8745 2 16 11 0.85 - - no Current
437 1.9686016829769004 -0.99422 -28.8284 5 16 0 0.00 - - no Open
384 2.550694247315306 -0.894788 -30.3438 9 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 -22.875kcal/mol
Ligand efficiency (LE) -0.6728kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.732
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 478.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.73
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 34.57kcal/mol
Minimised FF energy 3.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 771.4Ų
Total solvent-accessible surface area of free ligand
BSA total 529.7Ų
Buried surface area upon binding
BSA apolar 432.6Ų
Hydrophobic contacts buried
BSA polar 97.1Ų
Polar contacts buried
Fraction buried 68.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3223.9Ų
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 1473.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)