FAIRMol

Z56773008

Pose ID 11941 Compound 3551 Pose 420

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 Z56773008
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry high Native strong SASA done
Strain ΔE
22.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.42
Burial
67%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes
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 Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.691 kcal/mol/HA) ✓ Good fit quality (FQ -6.37) ✓ Good H-bonds (3 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (22.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (10)
Score
-17.970
kcal/mol
LE
-0.691
kcal/mol/HA
Fit Quality
-6.37
FQ (Leeson)
HAC
26
heavy atoms
MW
340
Da
LogP
4.07
cLogP
Final rank
1.2110
rank score
Inter norm
-0.837
normalised
Contacts
14
H-bonds 6
Strain ΔE
22.7 kcal/mol
SASA buried
67%
Lipo contact
82% BSA apolar/total
SASA unbound
594 Ų
Apolar buried
327 Ų

Interaction summary

HBD 2 HBA 1 HY 5 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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: permissive.
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
414 1.0527915152379248 -1.08767 -26.296 7 15 0 0.00 - - no Open
420 1.2109634167547734 -0.836536 -17.97 6 14 8 0.62 - - no Current
364 4.645977936063034 -1.1761 -30.1061 10 15 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 -17.970kcal/mol
Ligand efficiency (LE) -0.6912kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.368
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.07
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.40kcal/mol
Minimised FF energy 75.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 594.1Ų
Total solvent-accessible surface area of free ligand
BSA total 399.5Ų
Buried surface area upon binding
BSA apolar 327.3Ų
Hydrophobic contacts buried
BSA polar 72.2Ų
Polar contacts buried
Fraction buried 67.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3097.3Ų
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 1494.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)