FAIRMol

Z19455970

Pose ID 10649 Compound 2298 Pose 484

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand Z19455970
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.42, Jaccard 0.26
Burial
64%
Hydrophobic fit
60%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.738 kcal/mol/HA) ✓ Good fit quality (FQ -6.97) ✓ Good H-bonds (4 bonds) ✓ Good burial (64% SASA buried) ✗ Moderate strain (17.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-20.675
kcal/mol
LE
-0.738
kcal/mol/HA
Fit Quality
-6.97
FQ (Leeson)
HAC
28
heavy atoms
MW
419
Da
LogP
3.01
cLogP
Final rank
2.3883
rank score
Inter norm
-0.869
normalised
Contacts
12
H-bonds 5
Strain ΔE
17.4 kcal/mol
SASA buried
64%
Lipo contact
60% BSA apolar/total
SASA unbound
673 Ų
Apolar buried
256 Ų

Interaction summary

HBA 4 HY 4 PI 0 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap5Native recall0.42
Jaccard0.26RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT16Atoms7551
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
391 0.8112587710984578 -0.883156 -21.7804 4 19 0 0.00 - - no Open
388 1.761457712336876 -1.18388 -28.0949 12 17 0 0.00 - - no Open
484 2.388298171391906 -0.868572 -20.6754 5 12 5 0.42 - - no Current
101 2.911216982679596 -0.879119 -20.3872 5 13 5 0.42 - - no Open
95 2.970006987126121 -1.08769 -25.015 13 16 0 0.00 - - no Open
379 3.450130273935065 -0.998633 -22.0405 14 15 0 0.00 - - no Open
423 3.7405836219795368 -1.00578 -24.1953 10 15 0 0.00 - - no Open
160 3.885655564123343 -0.784425 -18.1914 7 14 0 0.00 - - no Open
100 4.225272845749715 -1.07342 -27.2468 7 13 0 0.00 - - no Open
73 5.143261743022093 -1.07475 -24.8662 12 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 -20.675kcal/mol
Ligand efficiency (LE) -0.7384kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.971
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 419.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.01
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -24.66kcal/mol
Minimised FF energy -42.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 673.0Ų
Total solvent-accessible surface area of free ligand
BSA total 429.7Ų
Buried surface area upon binding
BSA apolar 255.7Ų
Hydrophobic contacts buried
BSA polar 173.9Ų
Polar contacts buried
Fraction buried 63.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 59.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3075.0Ų
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 1477.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)