FAIRMol

Z19656430

Pose ID 8086 Compound 1827 Pose 634

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
T12
T. brucei R5P T. brucei
Ligand Z19656430
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
24.1 kcal/mol
Protein clashes
0
Internal clashes
6
Native overlap
contact recall 0.56, Jaccard 0.47, H-bond role recall 0.40
Burial
74%
Hydrophobic fit
77%
Reason: 6 internal clashes
6 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (10/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.047 kcal/mol/HA) ✓ Good fit quality (FQ -9.88) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ High strain energy (24.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-29.303
kcal/mol
LE
-1.047
kcal/mol/HA
Fit Quality
-9.88
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
3.23
cLogP
Final rank
4.4753
rank score
Inter norm
-1.025
normalised
Contacts
12
H-bonds 14
Strain ΔE
24.1 kcal/mol
SASA buried
74%
Lipo contact
77% BSA apolar/total
SASA unbound
631 Ų
Apolar buried
358 Ų

Interaction summary

HBA 11 HY 3 PI 3 CLASH 0

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
No clash · clashes detected for this pose.

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 overlap9Native recall0.56
Jaccard0.47RMSD-
HB strict6Strict recall0.50
HB same residue+role4HB role recall0.40
HB same residue5HB residue recall0.50

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
624 0.6825260708028559 -0.880028 -23.8957 2 17 0 0.00 0.00 - no Open
633 1.6318078139508165 -0.908922 -22.3664 2 13 0 0.00 0.00 - no Open
634 4.475257794976034 -1.02469 -29.3035 14 12 9 0.56 0.40 - 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 -29.303kcal/mol
Ligand efficiency (LE) -1.0466kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.880
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.23
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 96.75kcal/mol
Minimised FF energy 72.61kcal/mol

SASA & burial

✓ computed
SASA (unbound) 631.1Ų
Total solvent-accessible surface area of free ligand
BSA total 463.6Ų
Buried surface area upon binding
BSA apolar 357.7Ų
Hydrophobic contacts buried
BSA polar 105.9Ų
Polar contacts buried
Fraction buried 73.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2183.8Ų
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 777.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)