FAIRMol

Z25403655

Pose ID 13452 Compound 2987 Pose 573

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z25403655
PDB9IFH↗

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
29.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00
Burial
55%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.768
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.556
ADMET + ECO + DL
ADMETscore (GDS)
0.548
absorption · distr. · metab.
DLscore
0.445
drug-likeness
P(SAFE)
0.09
GDS classification
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.731 kcal/mol/HA) ✓ Good fit quality (FQ -6.97) ✓ Good H-bonds (5 bonds) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (29.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.187
kcal/mol
LE
-0.731
kcal/mol/HA
Fit Quality
-6.97
FQ (Leeson)
HAC
29
heavy atoms
MW
433
Da
LogP
2.66
cLogP
Final rank
2.9177
rank score
Inter norm
-0.734
normalised
Contacts
12
H-bonds 8
Strain ΔE
29.8 kcal/mol
SASA buried
55%
Lipo contact
70% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
267 Ų

Interaction summary

HBD 2 HBA 3 HY 4 PI 1 CLASH 3

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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.43RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:264; 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
560 0.4219802112234943 -1.115 -30.3827 5 14 0 0.00 0.00 - no Open
562 1.4283150224008307 -0.752873 -21.3542 9 10 0 0.00 0.00 - no Open
587 1.5034175836679107 -0.759669 -18.4209 8 12 0 0.00 0.00 - no Open
564 2.3157924979606697 -0.873015 -23.9565 4 14 0 0.00 0.00 - no Open
573 2.917700286713863 -0.733702 -21.1866 8 12 6 0.75 0.00 - no Current
578 2.9238356039284867 -0.81816 -24.7433 7 17 0 0.00 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 -21.187kcal/mol
Ligand efficiency (LE) -0.7306kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.974
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 432.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.66
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 47.70kcal/mol
Minimised FF energy 17.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.7Ų
Total solvent-accessible surface area of free ligand
BSA total 379.0Ų
Buried surface area upon binding
BSA apolar 267.2Ų
Hydrophobic contacts buried
BSA polar 111.8Ų
Polar contacts buried
Fraction buried 54.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3059.6Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1491.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)