FAIRMol

TC489

Pose ID 11785 Compound 1122 Pose 264

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 TC489
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
39.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.77, Jaccard 0.56
Burial
65%
Hydrophobic fit
87%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 63% of hydrophobic surface is solvent-exposed (19/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.540 kcal/mol/HA) ✓ Good fit quality (FQ -5.57) ✓ Good H-bonds (5 bonds) ✓ Good burial (65% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Very high strain energy (39.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-20.518
kcal/mol
LE
-0.540
kcal/mol/HA
Fit Quality
-5.57
FQ (Leeson)
HAC
38
heavy atoms
MW
516
Da
LogP
3.89
cLogP
Final rank
4.8452
rank score
Inter norm
-0.602
normalised
Contacts
15
H-bonds 6
Strain ΔE
39.3 kcal/mol
SASA buried
65%
Lipo contact
87% BSA apolar/total
SASA unbound
816 Ų
Apolar buried
461 Ų

Interaction summary

HBD 3 HBA 2 HY 7 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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 overlap10Native recall0.77
Jaccard0.56RMSD-
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
291 1.4078249954263844 -0.767107 -30.4751 5 20 0 0.00 - - no Open
264 4.845218036863834 -0.602005 -20.5177 6 15 10 0.77 - - no Current
241 5.349385339385592 -0.724881 -29.5472 15 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 -20.518kcal/mol
Ligand efficiency (LE) -0.5399kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.566
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 515.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.89
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 121.58kcal/mol
Minimised FF energy 82.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 816.5Ų
Total solvent-accessible surface area of free ligand
BSA total 529.9Ų
Buried surface area upon binding
BSA apolar 460.9Ų
Hydrophobic contacts buried
BSA polar 69.0Ų
Polar contacts buried
Fraction buried 64.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3299.1Ų
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 1471.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)