FAIRMol

Z56811438

Pose ID 7873 Compound 1280 Pose 421

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
T12
T. brucei R5P T. brucei
Ligand Z56811438
PDB6FXS↗

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
31.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.83, H-bond role recall 0.50
Burial
66%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
2 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 High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.653 kcal/mol/HA) ✓ Good fit quality (FQ -6.54) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (31.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-22.217
kcal/mol
LE
-0.653
kcal/mol/HA
Fit Quality
-6.54
FQ (Leeson)
HAC
34
heavy atoms
MW
524
Da
LogP
4.03
cLogP
Final rank
4.0712
rank score
Inter norm
-0.819
normalised
Contacts
17
H-bonds 12
Strain ΔE
31.1 kcal/mol
SASA buried
66%
Lipo contact
68% BSA apolar/total
SASA unbound
756 Ų
Apolar buried
344 Ų

Interaction summary

HBA 7 HY 4 PI 5 CLASH 2

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.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap15Native recall0.94
Jaccard0.83RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.50
HB same residue7HB residue recall0.70

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
463 2.3087885354320044 -0.849252 -22.4988 4 15 0 0.00 0.00 - no Open
481 2.7957054174014 -0.667396 -19.9692 7 21 0 0.00 0.00 - no Open
421 4.071177036007283 -0.818704 -22.2174 12 17 15 0.94 0.50 - 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 -22.217kcal/mol
Ligand efficiency (LE) -0.6535kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.538
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 523.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.03
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -21.85kcal/mol
Minimised FF energy -52.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 755.8Ų
Total solvent-accessible surface area of free ligand
BSA total 502.3Ų
Buried surface area upon binding
BSA apolar 343.6Ų
Hydrophobic contacts buried
BSA polar 158.6Ų
Polar contacts buried
Fraction buried 66.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2122.8Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 832.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)