FAIRMol

Z26484974

Pose ID 11382 Compound 4793 Pose 539

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z26484974
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
49.0 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.75, Jaccard 0.41, H-bond role recall 1.00
Burial
87%
Hydrophobic fit
78%
Reason: 1 severe internal clashes, 7 internal clashes, strain 49.0 kcal/mol
strain ΔE 49.0 kcal/mol 1 severe internal clashes 7 protein-contact clashes 7 intramolecular clashes
EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.482
ADMET + ECO + DL
ADMETscore (GDS)
0.570
absorption · distr. · metab.
DLscore
0.445
drug-likeness
P(SAFE)
0.77
GDS classification
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.498 kcal/mol/HA) ✓ Good fit quality (FQ -4.90) ✓ Good H-bonds (3 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (49.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-15.935
kcal/mol
LE
-0.498
kcal/mol/HA
Fit Quality
-4.90
FQ (Leeson)
HAC
32
heavy atoms
MW
472
Da
LogP
4.72
cLogP
Final rank
3.7796
rank score
Inter norm
-0.733
normalised
Contacts
19
H-bonds 6
Strain ΔE
49.0 kcal/mol
SASA buried
87%
Lipo contact
78% BSA apolar/total
SASA unbound
739 Ų
Apolar buried
502 Ų

Interaction summary

HBD 1 HBA 2 HY 8 PI 4 CLASH 7 Severe 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.41RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
539 3.779577258771246 -0.732621 -15.9353 6 19 9 0.75 1.00 - 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 -15.935kcal/mol
Ligand efficiency (LE) -0.4980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.897
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 471.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.72
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 49.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 112.98kcal/mol
Minimised FF energy 63.94kcal/mol

SASA & burial

✓ computed
SASA (unbound) 739.0Ų
Total solvent-accessible surface area of free ligand
BSA total 641.0Ų
Buried surface area upon binding
BSA apolar 501.8Ų
Hydrophobic contacts buried
BSA polar 139.2Ų
Polar contacts buried
Fraction buried 86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6606.7Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2050.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)